Functional genomics using crispr-cas systems, compositions, methods, knock out libraries and applications thereof

ABSTRACT

The present invention generally relates to compositions, methods applications and screens used in functional genomics that focus on gene function in a cell and that may use vector systems and other aspects related to Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas systems and components thereof. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for utilizing the CRISPR-Cas system.

RELATED APPLICATIONS AND INCORPORATION BY REFERENCE

This application is a continuation of US international applicationPCT/US2013/074800 filed Dec. 12, 2013, which claims benefit of andpriority to U.S. provisional patent application Nos. 61/736,527 filedDec. 12, 2012 and 61/802,174 filed Mar. 15, 2013.

Reference is also made to U.S. provisional patent application Nos.61/960,777 filed on Sep. 25, 2013 and 61/961,980 filed on Oct. 28, 2013.Reference is made to U.S. provisional patent applications 61/758,468;61/769,046; 61/802,174; 61/806,375; 61/814,263; 61/819,803 and61/828,130 filed on Jan. 30, 2013; Feb. 25, 2013; Mar. 15, 2013; Mar.28, 2013; Apr. 20, 2013; May 6, 2013 and May 28, 2013 respectively.Reference is also made to U.S. provisional patent applications61/836,123, 61/847,537, 61/862,355 and 61/871,301 filed on Jun. 17,2013; Jul. 17, 2013, Aug. 5, 2013 and Aug. 28, 2013 respectively.Reference is also made to U.S. provisional patent applications61/736,527 and 61/748,427 on Dec. 12, 2012 and Jan. 2, 2013,respectively. Reference is also made to U.S. provisional patentapplication 61/791,409 filed on Mar. 15, 2013. Reference is also made toU.S. provisional patent application 61/799,800 filed Mar. 15, 2013.Reference is also made to U.S. provisional patent applications61/835,931, 61/835,936, 61/836,127, 61/836,101, 61/836,080, and61/835,973 each filed Jun. 17, 2013.

The foregoing applications, and all documents cited therein or duringtheir prosecution (“appln cited documents”) and all documents cited orreferenced in the appln cited documents, and all documents cited orreferenced herein (“herein cited documents”), and all documents cited orreferenced in herein cited documents, together with any manufacturer'sinstructions, descriptions, product specifications, and product sheetsfor any products mentioned herein or in any document incorporated byreference herein, are hereby incorporated herein by reference, and maybe employed in the practice of the invention. More specifically, allreferenced documents are incorporated by reference to the same extent asif each individual document was specifically and individually indicatedto be incorporated by reference.

STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

This invention was made with government support under the NIH PioneerAward (1DP1MH100706) awarded by the National Institutes of Health. Thegovernment has certain rights in the invention.

FIELD OF THE INVENTION

The present invention generally relates to compositions, methods,applications and screens used in functional genomics that focus on genefunction in a cell and that may use vector systems and other aspectsrelated to Clustered Regularly Interspaced Short Palindromic Repeats(CRISPR)-Cas systems and components thereof.

BACKGROUND OF THE INVENTION

Recent advances in genome sequencing techniques and analysis methodshave significantly accelerated the ability to catalog and map geneticfactors associated with a diverse range of biological functions anddiseases. Functional genomics is a field of molecular biology that maybe considered to utilize the vast wealth of data produced by genomicprojects (such as genome sequencing projects) to describe gene (andprotein) functions and interactions. Contrary to classical genomics,functional genomics focuses on the dynamic aspects such as genetranscription, translation, and protein-protein interactions, as opposedto the static aspects of the genomic information such as DNA sequence orstructures, though these static aspects are very important andsupplement one's understanding of cellular and molecular mechanisms.Functional genomics attempts to answer questions about the function ofDNA at the levels of genes, RNA transcripts, and protein products. A keycharacteristic of functional genomics studies is a genome-wide approachto these questions, generally involving high-throughput methods ratherthan a more traditional “gene-by-gene” approach. Given the vastinventory of genes and genetic information it is advantageous to usegenetic screens to provide information of what these genes do, whatcellular pathways they are involved in and how any alteration in geneexpression can result in a particular biological process.

Functional genomic screens and libraries attempt to characterize genefunction in the context of living cells and hence are likely to generatebiologically significant data. There are three key elements for afunctional genomics screen: a good reagent to perturb the gene, a goodtissue culture model and a good readout of cell state. Good reagentsthat allow for precise genome targeting technologies are needed toenable systematic reverse engineering of causal genetic variations byallowing selective perturbation of individual genetic elements, as wellas to advance synthetic biology, biotechnological, and medicalapplications. Although genome-editing techniques such as designer zincfingers, transcription activator-like effectors (TALEs), or homingmeganucleases are available for producing targeted genome perturbations,there remains a need for new genome engineering technologies that areaffordable, easy to set up, scalable, and amenable to targeting multiplepositions within the eukaryotic genome.

SUMMARY OF THE INVENTION

The CRISPR-Cas system does not require the generation of customizedproteins to target specific sequences but rather a single Cas enzyme canbe programmed by a short RNA molecule to recognize a specific DNAtarget. Adding the CRISPR-Cas system to the repertoire of genomesequencing techniques and analysis methods may significantly simplifythe methodology and accelerate the ability to catalog and map geneticfactors associated with a diverse range of biological functions anddiseases. To utilize the CRISPR-Cas system effectively for genomeediting without deleterious effects, it is critical to understandaspects of engineering, optimization and tissue/organ specific deliveryof these genome engineering tools, which are aspects of the claimedinvention.

There exists a pressing need for alternative and robust systems andtechniques for sequence targeting with a wide array of applications.Aspects of this invention address this need and provide relatedadvantages. An exemplary CRISPR complex comprises a CRISPR enzymecomplexed with a guide sequence hybridized to a target sequence withinthe target polynucleotide. The guide sequence is linked to a tracr matesequence, which in turn hybridizes to a tracr sequence.

One aspect of the invention comprehends a genome wide library that maycomprise a plurality of CRISPR-Cas system guide RNAs that may compriseguide sequences that are capable of targeting a plurality of targetsequences in a plurality of genomic loci, wherein said targeting resultsin a knockout of gene function. This library may potentially compriseguide RNAs that target each and every gene in the genome of an organism.In some embodiments of the invention the organism or subject is aeukaryote (including mammal including human) or a non-human eukaryote ora non-human animal or a non-human mammal. In some embodiments, theorganism or subject is a non-human animal, and may be an arthropod, forexample, an insect, or may be a nematode. In some methods of theinvention the organism or subject is a plant. In some methods of theinvention the organism or subject is a mammal or a non-human mammal. Anon-human mammal may be for example a rodent (preferably a mouse or arat), an ungulate, or a primate. In some methods of the invention theorganism or subject is algae, including microalgae, or is a fungus.

In another aspect, the invention provides a method of generating a geneknockout cell library comprising introducing into each cell in apopulation of cells a vector system of one or more vectors that maycomprise an engineered, non-naturally occurring CRISPR-Cas systemcomprising I. a Cas protein, and II. one or more guide RNAs of thelibrary of the invention, wherein components I and II may be on the sameor on different vectors of the system, integrating components I and IIinto each cell, wherein the guide sequence targets a unique gene in eachcell,

wherein the Cas protein is operably linked to a regulatory element,wherein when transcribed, the guide RNA comprising the guide sequencedirects sequence-specific binding of a CRISPR-Cas system to a targetsequence in the genomic loci of the unique gene, inducing cleavage ofthe genomic loci by the Cas protein, and confirming different knockoutmutations in a plurality of unique genes in each cell of the populationof cells thereby generating a gene knockout cell library. In anembodiment of the invention, the Cas protein is a Cas9 protein. Inanother embodiment, the one or more vectors are plasmid vectors. In afurther embodiment, the regulatory element operably linked to the Casprotein is an inducible promoter, e.g. a doxycycline inducible promoter.The invention comprehends that the population of cells is a populationof eukaryotic cells, and in a preferred embodiment, the population ofcells is a population of embryonic stem (ES) cells. In anotherembodiment the confirming of different knockout mutations is by wholeexome sequencing. The invention also provides kits that comprise thegenome wide libraries mentioned herein. The kit may comprise a singlecontainer comprising vectors or plasmids comprising the library of theinvention. The kit may also comprise a panel comprising a selection ofunique CRISPR-Cas system guide RNAs comprising guide sequences from thelibrary of the invention, wherein the selection is indicative of aparticular physiological condition. The invention comprehends that thetargeting is of about 100 or more sequences, about 1000 or moresequences or about 20,000 or more sequences or the entire genome.Furthermore, a panel of target sequences may be focused on a relevant ordesirable pathway, such as an immune pathway or cell division.

In another aspect the invention provides for use of genome widelibraries for functional genomic studies. Such studies focus on thedynamic aspects such as gene transcription, translation, andprotein-protein interactions, as opposed to the static aspects of thegenomic information such as DNA sequence or structures, though thesestatic aspects are very important and supplement one's understanding ofcellular and molecular mechanisms. Functional genomics attempts toanswer questions about the function of DNA at the levels of genes, RNAtranscripts, and protein products. A key characteristic of functionalgenomics studies is a genome-wide approach to these questions, generallyinvolving high-throughput methods rather than a more traditional“gene-by-gene” approach. Given the vast inventory of genes and geneticinformation it is advantageous to use genetic screens to provideinformation of what these genes do, what cellular pathways they areinvolved in and how any alteration in gene expression can result inparticular biological process.

In one aspect, the invention provides methods for using one or moreelements of a CRISPR-Cas system. The CRISPR complex of the inventionprovides an effective means for modifying a target polynucleotide. TheCRISPR complex of the invention has a wide variety of utilitiesincluding modifying (e.g., deleting, inserting, translocating,inactivating, activating) a target polynucleotide in a multiplicity ofcell types in various tissues and organs. As such the CRISPR complex ofthe invention has a broad spectrum of applications in, e.g., gene orgenome editing, gene therapy, drug discovery, drug screening, diseasediagnosis, and prognosis.

Aspects of the invention relate to Cas9 enzymes having improved targetspecificity in a CRISPR-Cas9 system having guide RNAs having optimalactivity, smaller in length than wild-type Cas9 enzymes and nucleic acidmolecules coding therefor, and chimeric Cas9 enzymes, as well as methodsof improving the target specificity of a Cas9 enzyme or of designing aCRISPR-Cas9 system comprising designing or preparing guide RNAs havingoptimal activity and/or selecting or preparing a Cas9 enzyme having asmaller size or length than wild-type Cas9 whereby packaging a nucleicacid coding therefor into a delivery vector is advanced as there is lesscoding therefor in the delivery vector than for wild-type Cas9, and/orgenerating chimeric Cas9 enzymes.

Also provided are uses of the present sequences, vectors, enzymes orsystems, in medicine or in therapy. Also provided are uses of the samein gene or genome editing. Also provided are the present sequences,vectors, enzymes, or systems for use in medicine or in therapy; or foruse in gene or genome editing. Still further provided are uses of thepresent sequences, vectors, enzymes, or systems in the manufacture of amedicament.

In an additional aspect of the invention, a Cas9 enzyme may comprise oneor more mutations and may be used as a generic DNA binding protein withor without fusion to a functional domain. The mutations may beartificially introduced mutations or gain- or loss-of-functionmutations. The mutations may include but are not limited to mutations inone of the catalytic domains (D10 and H840) in the RuvC and HNHcatalytic domains, respectively. Further mutations have beencharacterized. In one aspect of the invention, the functional domain maybe a transcriptional activation domain, which may be VP64. In otheraspects of the invention, the functional domain may be a transcriptionalrepressor domain, which may be KRAB or SID4X. Other aspects of theinvention relate to the mutated Cas 9 enzyme being fused to domainswhich include but are not limited to a transcriptional activator,repressor, a recombinase, a transposase, a histone remodeler, ademethylase, a DNA methyltransferase, a cryptochrome, a lightinducible/controllable domain or a chemically inducible/controllabledomain.

In a further embodiment, the invention provides for methods to generatemutant tracrRNA and direct repeat sequences or mutant chimeric guidesequences that allow for enhancing performance of these RNAs in cells.Aspects of the invention also provide for selection of said sequences.

Aspects of the invention also provide for methods of simplifying thecloning and delivery of components of the CRISPR complex. In a preferredembodiment of the invention, a suitable promoter, such as the U6promoter, is amplified with a DNA oligo and added onto the guide RNA.The resulting PCR product can then be transfected into cells to driveexpression of the guide RNA. Aspects of the invention also relate to theguide RNA being transcribed in vitro or ordered from a synthesis companyand directly transfected.

In one aspect, the invention provides for methods to improve activity byusing a more active polymerase. In a preferred embodiment, theexpression of guide RNAs under the control of the T7 promoter is drivenby the expression of the T7 polymerase in the cell. In an advantageousembodiment, the cell is a eukaryotic cell. In a preferred embodiment theeukaryotic cell is a human cell. In a more preferred embodiment thehuman cell is a patient specific cell.

In one aspect, the invention provides for methods of reducing thetoxicity of Cas enzymes. In certain aspects, the Cas enzyme is any Cas9as described herein, for instance any naturally-occurring bacterial Cas9as well as any chimaeras, mutants, homologs or orthologs. In a preferredembodiment, the Cas9 is delivered into the cell in the form of mRNA.This allows for the transient expression of the enzyme thereby reducingtoxicity. In another preferred embodiment, the invention also providesfor methods of expressing Cas9 under the control of an induciblepromoter, and the constructs used therein.

In another aspect, the invention provides for methods of improving thein vivo applications of the CRISPR-Cas system. In the preferredembodiment, the Cas enzyme is wildtype Cas9 or any of the modifiedversions described herein, including any naturally-occurring bacterialCas9 as well as any chimaeras, mutants, homologs or orthologs. Anadvantageous aspect of the invention provides for the selection of Cas9homologs that are easily packaged into viral vectors for delivery. Cas9orthologs typically share the general organization of 3-4 RuvC domainsand a HNH domain. The 5′ most RuvC domain cleaves the non-complementarystrand, and the HNH domain cleaves the complementary strand. Allnotations are in reference to the guide sequence.

The catalytic residue in the 5′ RuvC domain is identified throughhomology comparison of the Cas9 of interest with other Cas9 orthologs(from S. pyogenes type II CRISPR locus, S. thermophilus CRISPR locus 1,S. thermophilus CRISPR locus 3, and Franciscilla novicida type II CRISPRlocus), and the conserved Asp residue (D10) is mutated to alanine toconvert Cas9 into a complementary-strand nicking enzyme. Similarly, theconserved His and Asn residues in the HNH domains are mutated to Alanineto convert Cas9 into a non-complementary-strand nicking enzyme. In someembodiments, both sets of mutations may be made, to convert Cas9 into anon-cutting enzyme.

In some embodiments, the CRISPR enzyme is a type I or III CRISPR enzyme,preferably a type II CRISPR enzyme. This type II CRISPR enzyme may beany Cas enzyme. A preferred Cas enzyme may be identified as Cas9 as thiscan refer to the general class of enzymes that share homology to thebiggest nuclease with multiple nuclease domains from the type II CRISPRsystem. Most preferably, the Cas9 enzyme is from, or is derived from,spCas9 or saCas9. By derived, Applicants mean that the derived enzyme islargely based, in the sense of having a high degree of sequence homologywith, a wildtype enzyme, but that it has been mutated (modified) in someway as described herein

It will be appreciated that the terms Cas and CRISPR enzyme aregenerally used herein interchangeably, unless otherwise apparent. Asmentioned above, many of the residue numberings used herein refer to theCas9 enzyme from the type II CRISPR locus in Streptococcus pyogenes.However, it will be appreciated that this invention includes many moreCas9s from other species of microbes, such as SpCas9, SaCas9, St1Cas9and so forth. Further examples are provided herein. The skilled personwill be able to determine appropriate corresponding residues in Cas9enzymes other than SpCas9 by comparison of the relevant amino acidsequences. Thus, where a specific amino acid replacement is referred tousing the SpCas9 numbering, then, unless the context makes it apparentthis is not intended to refer to other Cas9 enzymes, the disclosure isintended to encompass corresponding modifications in other Cas9 enzymes.

An example of a codon optimized sequence, in this instance optimized forhumans (i.e. being optimized for expression in humans) is providedherein, see the SaCas9 human codon optimized sequence. Whilst this ispreferred, it will be appreciated that other examples are possible andcodon optimization for a host species is known.

In further embodiments, the invention provides for methods of enhancingthe function of Cas9 by generating chimeric Cas9 proteins. Chimeric Cas9proteins may be new Cas9 containing fragments from more than onenaturally occurring Cas9. These methods may comprise fusing N-terminalfragments of one Cas9 homolog with C-terminal fragments of another Cas9homolog. These methods also allow for the selection of new propertiesdisplayed by the chimeric Cas9 proteins.

It will be appreciated that in the present methods, where the organismis an animal or a plant, the modification may occur ex vivo or in vitro,for instance in a cell culture and in some instances not in vivo. Inother embodiments, it may occur in vivo. Where the modification occursex vivo or in vitro, a modified cell may be used to generate a completeorganism, or a modified cell may be introduced or reintroduced into ahost organism.

In one aspect, the invention provides a method of modifying an organismor a non-human organism by manipulation of a target sequence in agenomic locus of interest comprising: delivering a non-naturallyoccurring or engineered composition comprising:

A)—I. a CRISPR-Cas system chimeric RNA (chiRNA) polynucleotide sequence,wherein the polynucleotide sequence comprises:(a) a guide sequence capable of hybridizing to a target sequence in aeukaryotic cell,(b) a tracr mate sequence, and(c) a tracr sequence, andII. a polynucleotide sequence encoding a CRISPR enzyme comprising atleast one or more nuclear localization sequences,wherein (a), (b) and (c) are arranged in a 5′ to 3′ orientation,wherein when transcribed, the tracr mate sequence hybridizes to thetracr sequence and the guide sequence directs sequence-specific bindingof a CRISPR complex to the target sequence, andwherein the CRISPR complex comprises the CRISPR enzyme complexed with(1) the guide sequence that is hybridized to the target sequence, and(2) the tracr mate sequence that is hybridized to the tracr sequence andthe polynucleotide sequence encoding a CRISPR enzyme is DNA or RNA,or(B) I. polynucleotides comprising:(a) a guide sequence capable of hybridizing to a target sequence in aeukaryotic cell, and(b) at least one or more tracr mate sequences,II. a polynucleotide sequence encoding a CRISPR enzyme, andIII. a polynucleotide sequence comprising a tracr sequence,wherein when transcribed, the tracr mate sequence hybridizes to thetracr sequence and the guide sequence directs sequence-specific bindingof a CRISPR complex to the target sequence, andwherein the CRISPR complex comprises the CRISPR enzyme complexed with(1) the guide sequence that is hybridized to the target sequence, and(2) the tracr mate sequence that is hybridized to the tracr sequence,and the polynucleotide sequence encoding a CRISPR enzyme is DNA or RNA.

Any or all of the polynucleotide sequence encoding a CRISPR enzyme,guide sequence, tracr mate sequence or tracr sequence, may be RNA. Thepolynucleotides encoding the sequence encoding a CRISPR enzyme, theguide sequence, tracr mate sequence or tracr sequence may be RNA and maybe delivered via liposomes, nanoparticles, exosomes, microvesicles, or agene-gun.

It will be appreciated that where reference is made to a polynucleotide,which is RNA and is said to ‘comprise’ a feature such as a tracr matesequence, the RNA sequence includes the feature. Where thepolynucleotide is DNA and is said to comprise a feature such as a tracrmate sequence, the DNA sequence is or can be transcribed into the RNAincluding the feature at issue. Where the feature is a protein, such asthe CRISPR enzyme, the DNA or RNA sequence referred to is, or can be,translated (and in the case of DNA transcribed first).

Accordingly, in certain embodiments the invention provides a method ofmodifying an organism, e.g., mammal including human or a non-humanmammal or organism by manipulation of a target sequence in a genomiclocus of interest comprising delivering a non-naturally occurring orengineered composition comprising a viral or plasmid vector systemcomprising one or more viral or plasmid vectors operably encoding acomposition for expression thereof, wherein the composition comprises:(A) a non-naturally occurring or engineered composition comprising avector system comprising one or more vectors comprising I. a firstregulatory element operably linked to a CRISPR-Cas system chimeric RNA(chiRNA) polynucleotide sequence, wherein the polynucleotide sequencecomprises (a) a guide sequence capable of hybridizing to a targetsequence in a eukaryotic cell, (b) a tracr mate sequence, and (c) atracr sequence, and II. a second regulatory element operably linked toan enzyme-coding sequence encoding a CRISPR enzyme comprising at leastone or more nuclear localization sequences (or optionally at least oneor more nuclear localization sequences as some embodiments can involveno NLS), wherein (a), (b) and (c) are arranged in a 5′ to 3′orientation, wherein components I and II are located on the same ordifferent vectors of the system, wherein when transcribed, the tracrmate sequence hybridizes to the tracr sequence and the guide sequencedirects sequence-specific binding of a CRISPR complex to the targetsequence, and wherein the CRISPR complex comprises the CRISPR enzymecomplexed with (1) the guide sequence that is hybridized to the targetsequence, and (2) the tracr mate sequence that is hybridized to thetracr sequence, or (B) a non-naturally occurring or engineeredcomposition comprising a vector system comprising one or more vectorscomprising I. a first regulatory element operably linked to (a) a guidesequence capable of hybridizing to a target sequence in a eukaryoticcell, and (b) at least one or more tracr mate sequences, II. a secondregulatory element operably linked to an enzyme-coding sequence encodinga CRISPR enzyme, and III. a third regulatory element operably linked toa tracr sequence, wherein components I, II and III are located on thesame or different vectors of the system, wherein when transcribed, thetracr mate sequence hybridizes to the tracr sequence and the guidesequence directs sequence-specific binding of a CRISPR complex to thetarget sequence, and wherein the CRISPR complex comprises the CRISPRenzyme complexed with (1) the guide sequence that is hybridized to thetarget sequence, and (2) the tracr mate sequence that is hybridized tothe tracr sequence. In some embodiments, components I, II and III arelocated on the same vector. In other embodiments, components I and IIare located on the same vector, while component III is located onanother vector. In other embodiments, components I and III are locatedon the same vector, while component II is located on another vector. Inother embodiments, components II and III are located on the same vector,while component I is located on another vector. In other embodiments,each of components I, II and III is located on different vectors. Theinvention also provides a viral or plasmid vector system as describedherein.

Preferably, the vector is a viral vector, such as a lenti- or baculo- orpreferably adeno-viral/adeno-associated viral vectors, but other meansof delivery are known (such as yeast systems, microvesicles, geneguns/means of attaching vectors to gold nanoparticles) and are provided.In some embodiments, one or more of the viral or plasmid vectors may bedelivered via liposomes, nanoparticles, exosomes, microvesicles, or agene-gun.

By manipulation of a target sequence, Applicants also mean theepigenetic manipulation of a target sequence. This may be of thechromatin state of a target sequence, such as by modification of themethylation state of the target sequence (i.e. addition or removal ofmethylation or methylation patterns or CpG islands), histonemodification, increasing or reducing accessibility to the targetsequence, or by promoting 3D folding.

It will be appreciated that where reference is made to a method ofmodifying an organism or mammal including human or a non-human mammal ororganism by manipulation of a target sequence in a genomic locus ofinterest, this may apply to the organism (or mammal) as a whole or justa single cell or population of cells from that organism (if the organismis multicellular). In the case of humans, for instance, Applicantsenvisage, inter alia, a single cell or a population of cells and thesemay preferably be modified ex vivo and then re-introduced. In this case,a biopsy or other tissue or biological fluid sample may be necessary.Stem cells are also particularly preferred in this regard. But, ofcourse, in vivo embodiments are also envisaged.

In certain embodiments the invention provides a method of treating orinhibiting a condition caused by a defect in a target sequence in agenomic locus of interest in a subject (e.g., mammal or human) or anon-human subject (e.g., mammal) in need thereof comprising modifyingthe subject or a non-human subject by manipulation of the targetsequence and wherein the condition is susceptible to treatment orinhibition by manipulation of the target sequence comprising providingtreatment comprising: delivering a non-naturally occurring or engineeredcomposition comprising an AAV or lentivirus vector system comprising oneor more AAV or lentivirus vectors operably encoding a composition forexpression thereof, wherein the target sequence is manipulated by thecomposition when expressed, wherein the composition comprises: (A) anon-naturally occurring or engineered composition comprising a vectorsystem comprising one or more vectors comprising I. a first regulatoryelement operably linked to a CRISPR-Cas system chimeric RNA (chiRNA)polynucleotide sequence, wherein the polynucleotide sequence comprises(a) a guide sequence capable of hybridizing to a target sequence in aeukaryotic cell, (b) a tracr mate sequence, and (c) a tracr sequence,and II. a second regulatory element operably linked to an enzyme-codingsequence encoding a CRISPR enzyme comprising at least one or morenuclear localization sequences (or optionally at least one or morenuclear localization sequences as some embodiments can involve no NLS)wherein (a), (b) and (c) are arranged in a 5′ to 3′ orientation, whereincomponents I and II are located on the same or different vectors of thesystem, wherein when transcribed, the tracr mate sequence hybridizes tothe tracr sequence and the guide sequence directs sequence-specificbinding of a CRISPR complex to the target sequence, and wherein theCRISPR complex comprises the CRISPR enzyme complexed with (1) the guidesequence that is hybridized to the target sequence, and (2) the tracrmate sequence that is hybridized to the tracr sequence, or (B) anon-naturally occurring or engineered composition comprising a vectorsystem comprising one or more vectors comprising I. a first regulatoryelement operably linked to (a) a guide sequence capable of hybridizingto a target sequence in a eukaryotic cell, and (b) at least one or moretracr mate sequences, II. a second regulatory element operably linked toan enzyme-coding sequence encoding a CRISPR enzyme, and III. a thirdregulatory element operably linked to a tracr sequence, whereincomponents I, II and III are located on the same or different vectors ofthe system, wherein when transcribed, the tracr mate sequence hybridizesto the tracr sequence and the guide sequence directs sequence-specificbinding of a CRISPR complex to the target sequence, and wherein theCRISPR complex comprises the CRISPR enzyme complexed with (1) the guidesequence that is hybridized to the target sequence, and (2) the tracrmate sequence that is hybridized to the tracr sequence. In someembodiments, components I, II and III are located on the same vector. Inother embodiments, components I and II are located on the same vector,while component III is located on another vector. In other embodiments,components I and III are located on the same vector, while component IIis located on another vector. In other embodiments, components II andIII are located on the same vector, while component I is located onanother vector. In other embodiments, each of components I, II and IIIis located on different vectors. The invention also provides a viral(e.g. AAV or lentivirus) vector system as described herein.

Some methods of the invention can include inducing expression. In somemethods of the invention the organism or subject is a eukaryote(including mammal including human) or a non-human eukaryote or anon-human animal or a non-human mammal. In some embodiments, theorganism or subject is a non-human animal, and may be an arthropod, forexample, an insect, or may be a nematode. In some methods of theinvention the organism or subject is a plant. In some methods of theinvention the organism or subject is a mammal or a non-human mammal. Anon-human mammal may be for example a rodent (preferably a mouse or arat), an ungulate, or a primate. In some methods of the invention theorganism or subject is algae, including microalgae, or is a fungus. Insome methods of the invention the viral vector is an AAV or alentivirus, and can be part of a vector system as described herein. Insome methods of the invention the CRISPR enzyme is a Cas9. In somemethods of the invention the expression of the guide sequence is underthe control of the T7 promoter and is driven by the expression of T7polymerase.

The invention in some embodiments comprehends a method of delivering aCRISPR enzyme comprising delivering to a cell mRNA encoding the CRISPRenzyme. In some of these methods the CRISPR enzyme is a Cas9.

The invention also provides methods of preparing the vector systems ofthe invention, in particular the viral vector systems as describedherein. The invention in some embodiments comprehends a method ofpreparing the AAV of the invention comprising transfecting plasmid(s)containing or consisting essentially of nucleic acid molecule(s) codingfor the AAV into AAV-infected cells, and supplying AAV rep and/or capobligatory for replication and packaging of the AAV. In some embodimentsthe AAV rep and/or cap obligatory for replication and packaging of theAAV are supplied by transfecting the cells with helper plasmid(s) orhelper virus(es). In some embodiments the helper virus is a poxvirus,adenovirus, herpesvirus or baculovirus. In some embodiments the poxvirusis a vaccinia virus. In some embodiments the cells are mammalian cells.And in some embodiments the cells are insect cells and the helper virusis baculovirus. In other embodiments, the virus is a lentivirus.

In plants, pathogens are often host-specific. For example, Fusariumoxyvsporum f. sp. lycopersici causes tomato wilt but attacks onlytomato, and F. oxysporum f. dianthii Puccinia graminis f. sp. triticiattacks only wheat. Plants have existing and induced defenses to resistmost pathogens. Mutations and recombination events across plantgenerations lead to genetic variability that gives rise tosusceptibility, especially as pathogens reproduce with more frequencythan plants. In plants there can be non-host resistance, e.g., the hostand pathogen are incompatible. There can also be Horizontal Resistance,e.g., partial resistance against all races of a pathogen, typicallycontrolled by many genes and Vertical Resistance, e.g., completeresistance to some races of a pathogen but not to other races, typicallycontrolled by a few genes. In a Gene-for-Gene level, plants andpathogens evolve together, and the genetic changes in one balancechanges in other. Accordingly, using Natural Variability, breederscombine most useful genes for Yield, Quality, Uniformity, Hardiness,Resistance. The sources of resistance genes include native or foreignVarieties, Heirloom Varieties, Wild Plant Relatives, and InducedMutations, e.g., treating plant material with mutagenic agents. Usingthe present invention, plant breeders are provided with a new tool toinduce mutations. Accordingly, one skilled in the art can analyze thegenome of sources of resistance genes, and in Varieties having desiredcharacteristics or traits employ the present invention to induce therise of resistance genes, with more precision than previous mutagenicagents and hence accelerate and improve plant breeding programs.

The invention further comprehends a composition of the invention or aCRISPR enzyme thereof (including or alternatively mRNA encoding theCRISPR enzyme) for use in medicine or in therapy. In some embodimentsthe invention comprehends a composition according to the invention or aCRISPR enzyme thereof (including or alternatively mRNA encoding theCRISPR enzyme) for use in a method according to the invention. In someembodiments the invention provides for the use of a composition of theinvention or a CRISPR enzyme thereof (including or alternatively mRNAencoding the CRISPR enzyme) in ex vivo gene or genome editing. Incertain embodiments the invention comprehends use of a composition ofthe invention or a CRISPR enzyme thereof (including or alternativelymRNA encoding the CRISPR enzyme) in the manufacture of a medicament forex vivo gene or genome editing or for use in a method according of theinvention. The invention comprehends in some embodiments a compositionof the invention or a CRISPR enzyme thereof (including or alternativelymRNA encoding the CRISPR enzyme), wherein the target sequence is flankedat its 3′ end by a PAM (protospacer adjacent motif) sequence comprising5′-motif, especially where the Cas9 is (or is derived from) S. pyogenesor S. aureus Cas9. For example, a suitable PAM is 5′-NRG or 5′-NNGRR(where N is any Nucleotide) for SpCas9 or SaCas9 enzymes (or derivedenzymes), respectively, as mentioned below.

It will be appreciated that SpCas9 or SaCas9 are those from or derivedfrom S. pyogenes or S. aureus Cas9.

Aspects of the invention comprehend improving the specificity of aCRISPR enzyme, e.g. Cas9, mediated gene targeting and reducing thelikelihood of off-target modification by the CRISPR enzyme, e.g. Cas9.The invention in some embodiments comprehends a method of modifying anorganism or a non-human organism with a reduction in likelihood ofoff-target modifications by manipulation of a first and a second targetsequence on opposite strands of a DNA duplex in a genomic locus ofinterest in a cell comprising delivering a non-naturally occurring orengineered composition comprising:

I. a first CRISPR-Cas system chimeric RNA (chiRNA) polynucleotidesequence,

wherein the first polynucleotide sequence comprises:(a) a first guide sequence capable of hybridizing to the first targetsequence,(b) a first tracr mate sequence, and(c) a first tracr sequence,

II. a second CRISPR-Cas system chiRNA polynucleotide sequence, whereinthe second polynucleotide sequence comprises:

(a) a second guide sequence capable of hybridizing to the second targetsequence,(b) a second tracr mate sequence, and(c) a second tracr sequence, and

III. a polynucleotide sequence encoding a CRISPR enzyme comprising atleast one or more nuclear localization sequences and comprising one ormore mutations, wherein (a), (b) and (c) are arranged in a 5′ to 3′orientation, wherein when transcribed, the first and the second tracrmate sequence hybridize to the first and second tracr sequencerespectively and the first and the second guide sequence directssequence-specific binding of a first and a second CRISPR complex to thefirst and second target sequences respectively, wherein the first CRISPRcomplex comprises the CRISPR enzyme complexed with (1) the first guidesequence that is hybridized to the first target sequence, and (2) thefirst tracr mate sequence that is hybridized to the first tracrsequence, wherein the second CRISPR complex comprises the CRISPR enzymecomplexed with (1) the second guide sequence that is hybridized to thesecond target sequence, and (2) the second tract mate sequence that ishybridized to the second tracr sequence, wherein the polynucleotidesequence encoding a CRISPR enzyme is DNA or RNA, and wherein the firstguide sequence directs cleavage of one strand of the DNA duplex near thefirst target sequence and the second guide sequence directs cleavage ofthe other strand near the second target sequence inducing a doublestrand break, thereby modifying the organism or the non-human organismwith a reduction in likelihood of off-target modifications.

In some methods of the invention any or all of the polynucleotidesequence encoding the CRISPR enzyme, the first and the second guidesequence, the first and the second tracr mate sequence or the first andthe second tracr sequence, is/are RNA. In further embodiments of theinvention the polynucleotides encoding the sequence encoding the CRISPRenzyme, the first and the second guide sequence, the first and thesecond tracr mate sequence or the first and the second tracr sequence,is/are RNA and are delivered via liposomes, nanoparticles, exosomes,microvesicles, or a gene-gun. In certain embodiments of the invention,the first and second tracr mate sequence share 100% identity and/or thefirst and second tracr sequence share 100% identity. In someembodiments, the polynucleotides may be comprised within a vector systemcomprising one or more vectors. In preferred embodiments of theinvention the CRISPR enzyme is a Cas9 enzyme, e.g. SpCas9. In an aspectof the invention the CRISPR enzyme comprises one or more mutations in acatalytic domain, wherein the one or more mutations are selected fromthe group consisting of D10A, E762A, H840A, N854A, N863A and D986A. In ahighly preferred embodiment the CRISPR enzyme has the D10A mutation. Inpreferred embodiments, the first CRISPR enzyme has one or more mutationssuch that the enzyme is a complementary strand nicking enzyme, and thesecond CRISPR enzyme has one or more mutations such that the enzyme is anon-complementary strand nicking enzyme. Alternatively the first enzymemay be a non-complementary strand nicking enzyme, and the second enzymemay be a complementary strand nicking enzyme.

In preferred methods of the invention the first guide sequence directingcleavage of one strand of the DNA duplex near the first target sequenceand the second guide sequence directing cleavage of the other strandnear the second target sequence results in a 5′ overhang. In embodimentsof the invention the 5′ overhang is at most 200 base pairs, preferablyat most 100 base pairs, or more preferably at most 50 base pairs. Inembodiments of the invention the 5′ overhang is at least 26 base pairs,preferably at least 30 base pairs or more preferably 34-50 base pairs.

The invention in some embodiments comprehends a method of modifying anorganism or a non-human organism with a reduction in likelihood ofoff-target modifications by manipulation of a first and a second targetsequence on opposite strands of a DNA duplex in a genomic locus ofinterest in a cell comprising delivering a non-naturally occurring orengineered composition comprising a vector system comprising one or morevectors comprising

I. a first regulatory element operably linked to

(a) a first guide sequence capable of hybridizing to the first targetsequence, and(b) at least one or more tracr mate sequences,

II. a second regulatory element operably linked to

(a) a second guide sequence capable of hybridizing to the second targetsequence, and(b) at least one or more tracr mate sequences,

III. a third regulatory element operably linked to an enzyme-codingsequence encoding a CRISPR enzyme, and

IV. a fourth regulatory element operably linked to a tracr sequence,

wherein components I, II, III and IV are located on the same ordifferent vectors of the system, when transcribed, the tracr matesequence hybridizes to the tracr sequence and the first and the secondguide sequence direct sequence-specific binding of a first and a secondCRISPR complex to the first and second target sequences respectively,wherein the first CRISPR complex comprises the CRISPR enzyme complexedwith (1) the first guide sequence that is hybridized to the first targetsequence, and (2) the tracr mate sequence that is hybridized to thetracr sequence, wherein the second CRISPR complex comprises the CRISPRenzyme complexed with (1) the second guide sequence that is hybridizedto the second target sequence, and (2) the tracr mate sequence that ishybridized to the tracr sequence, wherein the polynucleotide sequenceencoding a CRISPR enzyme is DNA or RNA, and wherein the first guidesequence directs cleavage of one strand of the DNA duplex near the firsttarget sequence and the second guide sequence directs cleavage of theother strand near the second target sequence inducing a double strandbreak, thereby modifying the organism or the non-human organism with areduction in likelihood of off-target modifications.

The invention also provides a vector system as described herein. Thesystem may comprise one, two, three or four different vectors.Components I, II, III and IV may thus be located on one, two, three orfour different vectors, and all combinations for possible locations ofthe components are herein envisaged, for example: components I, II, IIIand IV can be located on the same vector; components I, II, III and IVcan each be located on different vectors; components I, II, III and IVmay be located on a total of two or three different vectors, with allcombinations of locations envisaged, etc.

In some methods of the invention any or all of the polynucleotidesequence encoding the CRISPR enzyme, the first and the second guidesequence, the first and the second tracr mate sequence or the first andthe second tracr sequence, is/are RNA. In further embodiments of theinvention the first and second tracr mate sequence share 100% identityand/or the first and second tracr sequence share 100% identity. Inpreferred embodiments of the invention the CRISPR enzyme is a Cas9enzyme, e.g. SpCas9. In an aspect of the invention the CRISPR enzymecomprises one or more mutations in a catalytic domain, wherein the oneor more mutations are selected from the group consisting of D10A, E762A,H840A. N854A, N863A and D986A. In a highly preferred embodiment theCRISPR enzyme has the D10A mutation. In preferred embodiments, the firstCRISPR enzyme has one or more mutations such that the enzyme is acomplementary strand nicking enzyme, and the second CRISPR enzyme hasone or more mutations such that the enzyme is a non-complementary strandnicking enzyme. Alternatively the first enzyme may be anon-complementary strand nicking enzyme, and the second enzyme may be acomplementary strand nicking enzyme. In a further embodiment of theinvention, one or more of the viral vectors are delivered via liposomes,nanoparticles, exosomes, microvesicles, or a gene-gun.

In preferred methods of the invention the first guide sequence directingcleavage of one strand of the DNA duplex near the first target sequenceand the second guide sequence directing cleavage of other strand nearthe second target sequence results in a 5′ overhang. In embodiments ofthe invention the 5′ overhang is at most 200 base pairs, preferably atmost 100 base pairs, or more preferably at most 50 base pairs. Inembodiments of the invention the 5′ overhang is at least 26 base pairs,preferably at least 30 base pairs or more preferably 34-50 base pairs.

The invention in some embodiments comprehends a method of modifying agenomic locus of interest with a reduction in likelihood of off-targetmodifications by introducing into a cell containing and expressing adouble stranded DNA molecule encoding a gene product of interest anengineered, non-naturally occurring CRISPR-Cas system comprising a Casprotein having one or more mutations and two guide RNAs that target afirst strand and a second strand of the DNA molecule respectively,whereby the guide RNAs target the DNA molecule encoding the gene productand the Cas protein nicks each of the first strand and the second strandof the DNA molecule encoding the gene product, whereby expression of thegene product is altered; and, wherein the Cas protein and the two guideRNAs do not naturally occur together.

In preferred methods of the invention the Cas protein nicking each ofthe first strand and the second strand of the DNA molecule encoding thegene product results in a 5′ overhang. In embodiments of the inventionthe 5′ overhang is at most 200 base pairs, preferably at most 100 basepairs, or more preferably at most 50 base pairs. In embodiments of theinvention the 5′ overhang is at least 26 base pairs, preferably at least30 base pairs or more preferably 34-50 base pairs.

Embodiments of the invention also comprehend the guide RNAs comprising aguide sequence fused to a tracr mate sequence and a tracr sequence. Inan aspect of the invention the Cas protein is codon optimized forexpression in a eukaryotic cell, preferably a mammalian cell or a humancell. In further embodiments of the invention the Cas protein is a typeII CRISPR-Cas protein, e.g. a Cas 9 protein. In a highly preferredembodiment the Cas protein is a Cas9 protein, e.g. SpCas9. In aspects ofthe invention the Cas protein has one or more mutations selected fromthe group consisting of D10A, E762A, H840A, N854A, N863A and D986A. In ahighly preferred embodiment the Cas protein has the D10A mutation.

Aspects of the invention relate to the expression of the gene productbeing decreased or a template polynucleotide being further introducedinto the DNA molecule encoding the gene product or an interveningsequence being excised precisely by allowing the two 5′ overhangs toreanneal and ligate or the activity or function of the gene productbeing altered or the expression of the gene product being increased. Inan embodiment of the invention, the gene product is a protein.

The invention also comprehends an engineered, non-naturally occurringCRISPR-Cas system comprising a Cas protein having one or more mutationsand two guide RNAs that target a first strand and a second strandrespectively of a double stranded DNA molecule encoding a gene productin a cell, whereby the guide RNAs target the DNA molecule encoding thegene product and the Cas protein nicks each of the first strand and thesecond strand of the DNA molecule encoding the gene product, wherebyexpression of the gene product is altered; and, wherein the Cas proteinand the two guide RNAs do not naturally occur together.

In aspects of the invention the guide RNAs may comprise a guide sequencefused to a tracr mate sequence and a tracr sequence. In an embodiment ofthe invention the Cas protein is a type II CRISPR-Cas protein. In anaspect of the invention the Cas protein is codon optimized forexpression in a eukaryotic cell, preferably a mammalian cell or a humancell. In further embodiments of the invention the Cas protein is a typeII CRISPR-Cas protein, e.g. a Cas 9 protein. In a highly preferredembodiment the Cas protein is a Cas9 protein, e.g. SpCas9. In aspects ofthe invention the Cas protein has one or more mutations selected fromthe group consisting of D10A, E762A, H840A, N854A, N863A and D986A. In ahighly preferred embodiment the Cas protein has the D10A mutation.

Aspects of the invention relate to the expression of the gene productbeing decreased or a template polynucleotide being further introducedinto the DNA molecule encoding the gene product or an interveningsequence being excised precisely by allowing the two 5′ overhangs toreanneal and ligate or the activity or function of the gene productbeing altered or the expression of the gene product being increased. Inan embodiment of the invention, the gene product is a protein.

The invention also comprehends an engineered, non-naturally occurringvector system comprising one or more vectors comprising:

a) a first regulatory element operably linked to each of two CRISPR-Cassystem guide RNAs that target a first strand and a second strandrespectively of a double stranded DNA molecule encoding a gene product,b) a second regulatory element operably linked to a Cas protein,wherein components (a) and (b) are located on same or different vectorsof the system, whereby the guide RNAs target the DNA molecule encodingthe gene product and the Cas protein nicks each of the first strand andthe second strand of the DNA molecule encoding the gene product, wherebyexpression of the gene product is altered; and, wherein the Cas proteinand the two guide RNAs do not naturally occur together.

In aspects of the invention the guide RNAs may comprise a guide sequencefused to a tracr mate sequence and a tracr sequence. In an embodiment ofthe invention the Cas protein is a type II CRISPR-Cas protein. In anaspect of the invention the Cas protein is codon optimized forexpression in a eukaryotic cell, preferably a mammalian cell or a humancell. In further embodiments of the invention the Cas protein is a typeII CRISPR-Cas protein, e.g. a Cas 9 protein. In a highly preferredembodiment the Cas protein is a Cas9 protein, e.g. SpCas9. In aspects ofthe invention the Cas protein has one or more mutations selected fromthe group consisting of D10A, E762A, H840A, N854A, N863A and D986A. In ahighly preferred embodiment the Cas protein has the D10A mutation.

Aspects of the invention relate to the expression of the gene productbeing decreased or a template polynucleotide being further introducedinto the DNA molecule encoding the gene product or an interveningsequence being excised precisely by allowing the two 5′ overhangs toreanneal and ligate or the activity or function of the gene productbeing altered or the expression of the gene product being increased. Inan embodiment of the invention, the gene product is a protein. Inpreferred embodiments of the invention the vectors of the system areviral vectors. In a further embodiment, the vectors of the system aredelivered via liposomes, nanoparticles, exosomes, microvesicles, or agene-gun.

In one aspect, the invention provides a method of modifying a targetpolynucleotide in a eukaryotic cell. In some embodiments, the methodcomprises allowing a CRISPR complex to bind to the target polynucleotideto effect cleavage of said target polynucleotide thereby modifying thetarget polynucleotide, wherein the CRISPR complex comprises a CRISPRenzyme complexed with a guide sequence hybridized to a target sequencewithin said target polynucleotide, wherein said guide sequence is linkedto a tracr mate sequence which in turn hybridizes to a tracr sequence.In some embodiments, said cleavage comprises cleaving one or two strandsat the location of the target sequence by said CRISPR enzyme. In someembodiments, said cleavage results in decreased transcription of atarget gene. In some embodiments, the method further comprises repairingsaid cleaved target polynucleotide by homologous recombination with anexogenous template polynucleotide, wherein said repair results in amutation comprising an insertion, deletion, or substitution of one ormore nucleotides of said target polynucleotide. In some embodiments,said mutation results in one or more amino acid changes in a proteinexpressed from a gene comprising the target sequence. In someembodiments, the method further comprises delivering one or more vectorsto said eukaryotic cell, wherein the one or more vectors driveexpression of one or more of: the CRISPR enzyme, the guide sequencelinked to the tracr mate sequence, and the tracr sequence. In someembodiments, said vectors are delivered to the eukaryotic cell in asubject. In some embodiments, said modifying takes place in saideukaryotic cell in a cell culture. In some embodiments, the methodfurther comprises isolating said eukaryotic cell from a subject prior tosaid modifying. In some embodiments, the method further comprisesreturning said eukaryotic cell and/or cells derived therefrom to saidsubject.

In one aspect, the invention provides a method of modifying expressionof a polynucleotide in a eukaryotic cell. In some embodiments, themethod comprises allowing a CRISPR complex to bind to the polynucleotidesuch that said binding results in increased or decreased expression ofsaid polynucleotide; wherein the CRISPR complex comprises a CRISPRenzyme complexed with a guide sequence hybridized to a target sequencewithin said polynucleotide, wherein said guide sequence is linked to atracr mate sequence which in turn hybridizes to a tracr sequence. Insome embodiments, the method further comprises delivering one or morevectors to said eukaryotic cells, wherein the one or more vectors driveexpression of one or more of: the CRISPR enzyme, the guide sequencelinked to the tracr mate sequence, and the tracr sequence.

In one aspect, the invention provides a method of generating a modeleukaryotic cell comprising a mutated disease gene. In some embodiments,a disease gene is any gene associated with an increase in the risk ofhaving or developing a disease. In some embodiments, the methodcomprises (a) introducing one or more vectors into a eukaryotic cell,wherein the one or more vectors drive expression of one or more of: aCRISPR enzyme, a guide sequence linked to a tracr mate sequence, and atracr sequence; and (b) allowing a CRISPR complex to bind to a targetpolynucleotide to effect cleavage of the target polynucleotide withinsaid disease gene, wherein the CRISPR complex comprises the CRISPRenzyme complexed with (1) the guide sequence that is hybridized to thetarget sequence within the target polynucleotide, and (2) the tracr matesequence that is hybridized to the tracr sequence, thereby generating amodel eukaryotic cell comprising a mutated disease gene. In someembodiments, said cleavage comprises cleaving one or two strands at thelocation of the target sequence by said CRISPR enzyme. In someembodiments, said cleavage results in decreased transcription of atarget gene. In some embodiments, the method further comprises repairingsaid cleaved target polynucleotide by homologous recombination with anexogenous template polynucleotide, wherein said repair results in amutation comprising an insertion, deletion, or substitution of one ormore nucleotides of said target polynucleotide. In some embodiments,said mutation results in one or more amino acid changes in a proteinexpression from a gene comprising the target sequence.

In one aspect the invention provides for a method of selecting one ormore prokaryotic cell(s) by introducing one or more mutations in a genein the one or more prokaryotic cell (s), the method comprising:introducing one or more vectors into the prokaryotic cell (s), whereinthe one or more vectors drive expression of one or more of: a CRISPRenzyme, a guide sequence linked to a tracr mate sequence, a tracrsequence, and an editing template; wherein the editing templatecomprises the one or more mutations that abolish CRISPR enzyme cleavage;allowing homologous recombination of the editing template with thetarget polynucleotide in the cell(s) to be selected; allowing a CRISPRcomplex to bind to a target polynucleotide to effect cleavage of thetarget polynucleotide within said gene, wherein the CRISPR complexcomprises the CRISPR enzyme complexed with (1) the guide sequence thatis hybridized to the target sequence within the target polynucleotide,and (2) the tracr mate sequence that is hybridized to the tracrsequence, wherein binding of the CRISPR complex to the targetpolynucleotide induces cell death, thereby allowing one or moreprokaryotic cell(s) in which one or more mutations have been introducedto be selected. In a preferred embodiment, the CRISPR enzyme is Cas9. Inanother aspect of the invention the cell to be selected may be aeukaryotic cell. Aspects of the invention allow for selection ofspecific cells without requiring a selection marker or a two-stepprocess that may include a counter-selection system.

In one aspect, the invention provides for methods of modifying a targetpolynucleotide in a eukaryotic cell. In some embodiments, the methodcomprises allowing a CRISPR complex to bind to the target polynucleotideto effect cleavage of said target polynucleotide thereby modifying thetarget polynucleotide, wherein the CRISPR complex comprises a CRISPRenzyme complexed with a guide sequence hybridized to a target sequencewithin said target polynucleotide, wherein said guide sequence is linkedto a tracr mate sequence which in turn hybridizes to a tracr sequence.

In other embodiments, this invention provides a method of modifyingexpression of a polynucleotide in a eukaryotic cell. The methodcomprises increasing or decreasing expression of a target polynucleotideby using a CRISPR complex that binds to the polynucleotide.

Where desired, to effect the modification of the expression in a cell,one or more vectors comprising a tracr sequence, a guide sequence linkedto the tracr mate sequence, a sequence encoding a CRISPR enzyme isdelivered to a cell. In some methods, the one or more vectors comprisesa regulatory element operably linked to an enzyme-coding sequenceencoding said CRISPR enzyme comprising a nuclear localization sequence;and a regulatory element operably linked to a tracr mate sequence andone or more insertion sites for inserting a guide sequence upstream ofthe tracr mate sequence. When expressed, the guide sequence directssequence-specific binding of a CRISPR complex to a target sequence in acell. Typically, the CRISPR complex comprises a CRISPR enzyme complexedwith (1) the guide sequence that is hybridized to the target sequence,and (2) the tracr mate sequence that is hybridized to the tracrsequence.

In some methods, a target polynucleotide can be inactivated to effectthe modification of the expression in a cell. For example, upon thebinding of a CRISPR complex to a target sequence in a cell, the targetpolynucleotide is inactivated such that the sequence is not transcribed,the coded protein is not produced, or the sequence does not function asthe wild-type sequence does. For example, a protein or microRNA codingsequence may be inactivated such that the protein is not produced.

In certain embodiments, the CRISPR enzyme comprises one or moremutations selected from the group consisting of D10A, E762A. H840A,N854A, N863A or D986A and/or the one or more mutations is in a RuvC1 orHNH domain of the CRISPR enzyme or is a mutation as otherwise asdiscussed herein. In some embodiments, the CRISPR enzyme has one or moremutations in a catalytic domain, wherein when transcribed, the tracrmate sequence hybridizes to the tracr sequence and the guide sequencedirects sequence-specific binding of a CRISPR complex to the targetsequence, and wherein the enzyme further comprises a functional domain.In some embodiments, the functional domain is a transcriptionalactivation domain, preferably VP64. In some embodiments, the functionaldomain is a transcription repression domain, preferably KRAB. In someembodiments, the transcription repression domain is SID, or concatemersof SID (eg SID4X). In some embodiments, the functional domain is anepigenetic modifying domain, such that an epigenetic modifying enzyme isprovided. In some embodiments, the functional domain is an activationdomain, which may be the P65 activation domain.

In some embodiments, the CRISPR enzyme is a type I or III CRISPR enzyme,but is preferably a type II CRISPR enzyme. This type II CRISPR enzymemay be any Cas enzyme. A Cas enzyme may be identified as Cas9 as thiscan refer to the general class of enzymes that share homology to thebiggest nuclease with multiple nuclease domains from the type II CRISPRsystem. Most preferably, the Cas9 enzyme is from, or is derived from,spCas9 or saCas9. By derived, Applicants mean that the derived enzyme islargely based, in the sense of having a high degree of sequence homologywith, a wildtype enzyme, but that it has been mutated (modified) in someway as described herein.

It will be appreciated that the terms Cas and CRISPR enzyme aregenerally used herein interchangeably, unless otherwise apparent. Asmentioned above, many of the residue numberings used herein refer to theCas9 enzyme from the type II CRISPR locus in Streptococcus pyogenes.However, it will be appreciated that this invention includes many moreCas9s from other species of microbes, such as SpCas9, SaCa9, St1Cas9 andso forth.

An example of a codon optimized sequence, in this instance optimized forhumans (i.e. being optimized for expression in humans) is providedherein, see the SaCas9 human codon optimized sequence. Whilst this ispreferred, it will be appreciated that other examples are possible andcodon optimization for a host species is known.

Preferably, delivery is in the form of a vector which may be a viralvector, such as a lenti- or baculo- or preferablyadeno-viral/adeno-associated viral vectors, but other means of deliveryare known (such as yeast systems, microvesicles, gene guns/means ofattaching vectors to gold nanoparticles) and are provided. A vector maymean not only a viral or yeast system (for instance, where the nucleicacids of interest may be operably linked to and under the control of (interms of expression, such as to ultimately provide a processed RNA) apromoter), but also direct delivery of nucleic acids into a host cell.While in herein methods the vector may be a viral vector and this isadvantageously an AAV, other viral vectors as herein discussed can beemployed, such as lentivirus. For example, baculoviruses may be used forexpression in insect cells. These insect cells may, in turn be usefulfor producing large quantities of further vectors, such as AAV orlentivirus vectors adapted for delivery of the present invention. Alsoenvisaged is a method of delivering the present CRISPR enzyme comprisingdelivering to a cell mRNA encoding the CRISPR enzyme. It will beappreciated that in certain embodiments the CRISPR enzyme is truncated,and/or comprised of less than one thousand amino acids or less than fourthousand amino acids, and/or is a nuclease or nickase, and/or iscodon-optimized, and/or comprises one or more mutations, and/orcomprises a chimeric CRISPR enzyme, and/or the other options as hereindiscussed. AAV and lentiviral vectors are preferred.

In certain embodiments, the target sequence is flanked or followed, atits 3′ end, by a PAM suitable for the CRISPR enzyme, typically a Cas andin particular a Cas9.

For example, a suitable PAM is 5′-NRG or 5′-NNGRR for SpCas9 or SaCas9enzymes (or derived enzymes), respectively.

It will be appreciated that SpCas9 or SaCas9 are those from or derivedfrom S. pyogenes or S. aureus Cas9.

Accordingly, it is an object of the invention to not encompass withinthe invention any previously known product, process of making theproduct, or method of using the product such that Applicants reserve theright and hereby disclose a disclaimer of any previously known product,process, or method. It is further noted that the invention does notintend to encompass within the scope of the invention any product,process, or making of the product or method of using the product, whichdoes not meet the written description and enablement requirements of theUSPTO (35 U.S.C. §112, first paragraph) or the EPO (Article 83 of theEPC), such that Applicants reserve the right and hereby disclose adisclaimer of any previously described product, process of making theproduct, or method of using the product.

It is noted that in this disclosure and particularly in the claimsand/or paragraphs, terms such as “comprises”, “comprised”, “comprising”and the like can have the meaning attributed to it in U.S. Patent law;e.g., they can mean “includes”, “included”, “including”, and the like;and that terms such as “consisting essentially of” and “consistsessentially of” have the meaning ascribed to them in U.S. Patent law,e.g., they allow for elements not explicitly recited, but excludeelements that are found in the prior art or that affect a basic or novelcharacteristic of the invention.

These and other embodiments are disclosed or are obvious from andencompassed by, the following Detailed Description.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity inthe appended claims. A better understanding of the features andadvantages of the present invention will be obtained by reference to thefollowing detailed description that sets forth illustrative embodiments,in which the principles of the invention are utilized, and theaccompanying drawings of which:

FIG. 1 shows a schematic model of the CRISPR system. The Cas9 nucleasefrom Streptococcus pyogenes (yellow) is targeted to genomic DNA by asynthetic guide RNA (sgRNA) consisting of a 20-nt guide sequence (blue)and a scaffold (red). The guide sequence base-pairs with the DNA target(blue), directly upstream of a requisite 5′-NGG protospacer adjacentmotif (PAM; magenta), and Cas9 mediates a double-stranded break (DSB)-3bp upstream of the PAM (red triangle).

FIG. 2A-F shows an exemplary CRISPR system, a possible mechanism ofaction, an example adaptation for expression in eukaryotic cells, andresults of tests assessing nuclear localization and CRISPR activity.

FIG. 3A-D shows results of an evaluation of SpCas9 specificity for anexample target.

FIG. 4A-G show an exemplary vector system and results for its use indirecting homologous recombination in eukaryotic cells.

FIG. 5 provides a table of protospacer sequences and summarizesmodification efficiency results for protospacer targets designed basedon exemplary S. pyogenes and S. thermophilus CRISPR systems withcorresponding PAMs against loci in human and mouse genomes. Cells weretransfected with Cas9 and either pre-crRNA/tracrRNA or chimeric RNA, andanalyzed 72 hours after transfection. Percent indels are calculatedbased on Surveyor assay results from indicated cell lines (N=3 for allprotospacer targets, errors are S.E.M., N.D. indicates not detectableusing the Surveyor assay, and N.T. indicates not tested in this study).

FIG. 6A-C shows a comparison of different tracrRNA transcripts forCas9-mediated gene targeting.

FIG. 7 shows a schematic of a surveyor nuclease assay for detection ofdouble strand break-induced micro-insertions and -deletions.

FIG. 8A-B shows exemplary bicistronic expression vectors for expressionof CRISPR system elements in eukaryotic cells.

FIG. 9A-C shows histograms of distances between adjacent S. pyogenesSF370 locus 1 PAM (NGG) (FIG. 9A) and S. thermophilus LMD9 locus 2 PAM(NNAGAAW) (FIG. 9B) in the human genome; and distances for each PAM bychromosome (Chr) (FIG. 9C).

FIG. 10A-D shows an exemplary CRISPR system, an example adaptation forexpression in eukaryotic cells, and results of tests assessing CRISPRactivity.

FIG. 11A-C shows exemplary manipulations of a CRISPR system fortargeting of genomic loci in mammalian cells.

FIG. 12A-B shows the results of a Northern blot analysis of crRNAprocessing in mammalian cells.

FIG. 13A-B shows an exemplary selection of protospacers in the humanPVALB and mouse Th loci.

FIG. 14 shows example protospacer and corresponding PAM sequence targetsof the S. thermophilus CRISPR system in the human EMX1 locus.

FIG. 15 provides a table of sequences for primers and probes used forSurveyor, RFLP, genomic sequencing, and Northern blot assays.

FIG. 16A-C shows exemplary manipulation of a CRISPR system with chimericRNAs and results of SURVEYOR assays for system activity in eukaryoticcells.

FIG. 17A-B shows a graphical representation of the results of SURVEYORassays for CRISPR system activity in eukaryotic cells.

FIG. 18 shows an exemplary visualization of some S. pyogenes Cas9 targetsites in the human genome using the UCSC genome browser.

FIG. 19A-D shows a circular depiction of the phylogenetic analysisrevealing five families of Cas9s, including three groups of large Cas9s(˜1400 amino acids) and two of small Cas9s (˜1100 amino acids).

FIG. 20A-F shows the linear depiction of the phylogenetic analysisrevealing five families of Cas9s, including three groups of large Cas9s(˜1400 amino acids) and two of small Cas9s (˜1100 amino acids).

FIG. 21A-D shows genome editing via homologous recombination. (a)Schematic of SpCas9 nickase, with D10A mutation in the RuvC I catalyticdomain. (b) Schematic representing homologous recombination (HR) at thehuman EMX1 locus using either sense or antisense single strandedoligonucleotides as repair templates. Red arrow above indicates sgRNAcleavage site; PCR primers for genotyping (Tables J and K) are indicatedas arrows in right panel. (c) Sequence of region modified by HR. d,SURVEYOR assay for wildtype (wt) and nickase (D10A) SpCas9-mediatedindels at the EMX1 target 1 locus (n=3). Arrows indicate positions ofexpected fragment sizes.

FIG. 22A-B shows single vector designs for SpCas9.

FIG. 23 shows a graph representing the length distribution of Cas9orthologs.

FIG. 24A-M shows sequences where the mutation points are located withinthe SpCas9 gene.

FIG. 25A shows the Conditional Cas9, Rosa26 targeting vector map.

FIG. 25B shows the Constitutive Cas9, Rosa26 targeting vector map.

FIG. 26 shows a schematic of the important elements in the Constitutiveand Conditional Cas9 constructs.

FIG. 27 shows delivery and in vivo mouse brain Cas9 expression data.

FIG. 28 shows RNA delivery of Cas9 and chimeric RNA into cells (A)Delivery of a GFP reporter as either DNA or mRNA into Neuro-2A cells.(B) Delivery of Cas9 and chimeric RNA against the Icam2 gene as RNAresults in cutting for one of two spacers tested. (C) Delivery of Cas9and chimeric RNA against the F7 gene as RNA results in cutting for oneof two spacers tested.

FIG. 29 shows how DNA double-strand break (DSB) repair promotes geneediting. In the error-prone non-homologous end joining (NHEJ) pathway,the ends of a DSB are processed by endogenous DNA repair machineries andrejoined together, which can result in random insertion/deletion (indel)mutations at the site of junction. Indel mutations occurring within thecoding region of a gene can result in frame-shift and a premature stopcodon, leading to gene knockout. Alternatively, a repair template in theform of a plasmid or single-stranded oligodeoxynucleotides (ssODN) canbe supplied to leverage the homology-directed repair (HDR) pathway,which allows high fidelity and precise editing.

FIG. 30A-C shows anticipated results for HDR in HEK and HUES9 cells. (a)Either a targeting plasmid or an ssODN (sense or antisense) withhomology arms can be used to edit the sequence at a target genomic locuscleaved by Cas9 (red triangle). To assay the efficiency of HDR, weintroduced a HindIII site (red bar) into the target locus, which wasPCR-amplified with primers that anneal outside of the region ofhomology. Digestion of the PCR product with HindIII reveals theoccurrence of HDR events. (b) ssODNs, oriented in either the sense orthe antisense (s or a) direction relative to the locus of interest, canbe used in combination with Cas9 to achieve efficient HDR-mediatedediting at the target locus. A minimal homology region of 40 bp, andpreferably 90 bp, is recommended on either side of the modification (redbar). (c) Example of the effect of ssODNs on HDR in the EMX1 locus isshown using both wild-type Cas9 and Cas9 nickase (D10A). Each ssODNcontains homology arms of 90 bp flanking a 12-bp insertion of tworestriction sites.

FIG. 31A-C shows the repair strategy for Cystic Fibrosis delta F508mutation.

FIG. 32A-B (a) shows a schematic of the GAA repeat expansion in FXNintron 1 and (b) shows a schematic of the strategy adopted to excise theGAA expansion region using the CRISPR/Cas system.

FIG. 33 shows a screen for efficient SpCas9 mediated targeting of Tet1-3and Dnmt1, 3a and 3b gene loci. Surveyor assay on DNA from transfectedN2A cells demonstrates efficient DNA cleavage by using different gRNAs.

FIG. 34 shows a strategy of multiplex genome targeting using a 2-vectorsystem in an AAV1/2 delivery system. Tet1-3 and Dnmt1, 3a and 3b gRNAunder the control of the U6 promoter. GFP-KASH under the control of thehuman synapsin promoter. Restriction sides shows simple gRNA replacementstrategy by subcloning. HA-tagged SpCas9 flanked by two nuclearlocalization signals (NLS) is shown. Both vectors are delivered into thebrain by AAV1/2 virus in a 1:1 ratio.

FIG. 35 shows verification of multiplex DNMT targeting vector #1functionality using Surveyor assay. N2A cells were co-transfected withthe DNMT targeting vector #1 (+) and the SpCas9 encoding vector fortesting SpCas9 mediated cleavage of DNMTs genes family loci. gRNA only(−) is negative control. Cells were harvested for DNA purification anddownstream processing 48 h after transfection.

FIG. 36 shows verification of multiplex DNMT targeting vector #2functionality using Surveyor assay. N2A cells were co-transfected withthe DNMT targeting vector #1 (+) and the SpCas9 encoding vector fortesting SpCas9 mediated cleavage of DNMTs genes family loci. gRNA only(−) is negative control. Cells were harvested for DNA purification anddownstream processing 48 h after transfection.

FIG. 37 shows schematic overview of short promoters and short polyAversions used for HA-SpCas9 expression in vivo. Sizes of the encodingregion from L-ITR to R-ITR are shown on the right.

FIG. 38 shows schematic overview of short promoters and short polyAversions used for HA-SaCas9 expression in vivo. Sizes of the encodingregion from L-ITR to R-ITR are shown on the right.

FIG. 39 shows expression of SpCas9 and SaCas9 in N2A cells.Representative Western blot of HA-tagged SpCas9 and SaCas9 versionsunder the control of different short promoters and with or short polyA(spA) sequences. Tubulin is loading control. mCherry (mCh) is atransfection control. Cells were harvested and further processed forWestern blotting 48 h after transfection.

FIG. 40 shows screen for efficient SaCas9 mediated targeting of Tet3gene locus. Surveyor assay on DNA from transfected N2A cellsdemonstrates efficient DNA cleavage by using different gRNAs with NNGGGTPUM sequence. GFP transfected cells and cells expressing only SaCas9 arecontrols.

FIG. 41 shows expression of HA-SaCas9 in the mouse brain. Animals wereinjected into dentate gyri with virus driving expression of HA-SaCas9under the control of human Synapsin promoter. Animals were sacrificed 2weeks after surgery. HA tag was detected using rabbit monoclonalantibody C29F4 (Cell Signaling). Cell nuclei stained in blue with DAPIstain.

FIG. 42 shows expression of SpCas9 and SaCas9 in cortical primaryneurons in culture 7 days after transduction. Representative Westernblot of HA-tagged SpCas9 and SaCas9 versions under the control ofdifferent promoters and with bgh or short polyA (spA) sequences. Tubulinis loading control.

FIG. 43 shows LIVE/DEAD stain of primary cortical neurons 7 days aftertransduction with AAV1 particles carrying SpCas9 with differentpromoters and multiplex gRNAs constructs (example shown on the lastpanel for DNMTs). Neurons after AAV transduction were compared withcontrol untransduced neurons. Red nuclei indicate permeabilized, deadcells (second line of panels). Live cells are marked in green color(third line of panels).

FIG. 44 shows LIVE/DEAD stain of primary cortical neurons 7 days aftertransduction with AAV1 particles carrying SaCas9 with differentpromoters. Red nuclei indicate permeabilized, dead cells (second line ofpanels). Live cells are marked in green color (third line of panels).

FIG. 45 shows comparison of morphology of neurons after transductionwith AAV1 virus carrying SpCas9 and gRNA multiplexes for TETs and DNMTsgenes loci. Neurons without transduction are shown as a control.

FIG. 46 shows verification of multiplex DNMT targeting vector #1functionality using Surveyor assay in primary cortical neurons. Cellswere co-transduced with the DNMT targeting vector #1 and the SpCas9viruses with different promoters for testing SpCas9 mediated cleavage ofDNMTs genes family loci.

FIG. 47 shows in vivo efficiency of SpCas9 cleavage in the brain. Micewere injected with AAV1/2 virus carrying gRNA multiplex targeting DNMTfamily genes loci together with SpCas9 viruses under control of 2different promoters: mouse Mecp2 and rat Map1b. Two weeks afterinjection brain tissue was extracted and nuclei were prepped and sortedusing FACS, based on the GFP expression driven by Synapsin promoter fromgRNA multiplex construct. After gDNA extraction Surveyor assay wasrun. + indicates GFP positive nuclei and − control, GFP-negative nucleifrom the same animal. Numbers on the gel indicate assessed SpCas9efficiency.

FIG. 48 shows purification of GFP-KASH labeled cell nuclei fromhippocampal neurons. The outer nuclear membrane (ONM) of the cellnuclear membrane is tagged with a fusion of GFP and the KASH proteintransmembrane domain. Strong GFP expression in the brain after one weekof stereotactic surgery and AAV1/2 injection. Density gradientcentrifugation step to purify cell nuclei from intact brain. Purifiednuclei are shown. Chromatin stain by Vybrant® DyeCycle™ Ruby Stain isshown in red, GFP labeled nuclei are green. Representative FACS profileof GFP+ and GFP− cell nuclei (Magenta: Vybrant® DyeCycle™ Ruby Stain,Green: GFP).

FIG. 49 shows efficiency of SpCas9 cleavage in the mouse brain. Micewere injected with AAV1/2 virus carrying gRNA multiplex targeting TETfamily genes loci together with SpCas9 viruses under control of 2different promoters: mouse Mecp2 and rat Map1b. Three weeks afterinjection brain tissue was extracted, nuclei were prepped and sortedusing FACS, based on the GFP expression driven by Synapsin promoter fromgRNA multiplex construct. After gDNA extraction Surveyor assay wasrun. + indicates GFP positive nuclei and − control, GFP-negative nucleifrom the same animal. Numbers on the gel indicate assessed SpCas9efficiency.

FIG. 50 shows GFP-KASH expression in cortical neurons in culture.Neurons were transduced with AAV1 virus carrying gRNA multiplexconstructs targeting TET genes loci. The strongest signal localizearound cells nuclei due to KASH domain localization.

FIG. 51 shows (top) a list of spacing (as indicated by the pattern ofarrangement for two PAM sequences) between pairs of guide RNAs. Onlyguide RNA pairs satisfying patterns 1, 2, 3, 4 exhibited indels whenused with SpCas9(D10A) nickase. (bottom) Gel images showing thatcombination of SpCas9(D10A) with pairs of guide RNA satisfying patterns1, 2, 3, 4 led to the formation of indels in the target site.

FIG. 52 shows a list of U6 reverse primer sequences used to generateU6-guide RNA expression cassettes. Each primer needs to be paired withthe U6 forward primer “gcactgagggcctatttcccatgattc” to generateamplicons containing U6 and the desired guide RNA.

FIG. 53 shows a Genomic sequence map from the human Emx1 locus showingthe locations of the 24 patterns listed in FIG. 33.

FIG. 54 shows on (right) a gel image indicating the formation of indelsat the target site when variable 5′ overhangs are present after cleavageby the Cas9 nickase targeted by different pairs of guide RNAs. on (left)a table indicating the lane numbers of the gel on the right and variousparameters including identifying the guide RNA pairs used and the lengthof the 5′ overhang present following cleavage by the Cas9 nickase.

FIG. 55 shows a Genomic sequence map from the human Emx1 locus showingthe locations of the different pairs of guide RNAs that result in thegel patterns of FIG. 54 (right) and which are further described inExample 35.

The figures herein are for illustrative purposes only and are notnecessarily drawn to scale.

DETAILED DESCRIPTION OF THE INVENTION

The invention relates to the engineering and optimization of systems,methods and compositions used for the control of gene expressioninvolving sequence targeting, such as genome perturbation orgene-editing, that relate to the CRISPR-Cas system and componentsthereof. In advantageous embodiments, the Cas enzyme is Cas9.

An advantage of the present methods is that the CRISPR system avoidsoff-target binding and its resulting side effects. This is achievedusing systems arranged to have a high degree of sequence specificity forthe target DNA.

Cas9 optimization may be used to enhance function or to develop newfunctions, one can generate chimeric Cas9 proteins. Examples that theApplicants have generated are provided in Example 12. Chimeric Cas9proteins can be made by combining fragments from different Cas9homologs. For example, two example chimeric Cas9 proteins from the Cas9sdescribed herein. For example, Applicants fused the N-term of St1Cas9(fragment from this protein is in bold) with C-term of SpCas9. Thebenefit of making chimeric Cas9s include any or all of: reducedtoxicity, improved expression in eukaryotic cells; enhanced specificity;reduced molecular weight of protein, for example, making the proteinsmaller by combining the smallest domains from different Cas9 homologs;and/or altering the PAM sequence requirement.

The Cas9 may be used as a generic DNA binding protein. For example, andas shown in Example 13, Applicants used Cas9 as a generic DNA bindingprotein by mutating the two catalytic domains (D10 and H840) responsiblefor cleaving both strands of the DNA target. In order to upregulate genetranscription at a target locus Applicants fused a transcriptionalactivation domain (VP64) to Cas9. Other transcriptional activationdomains are known. As shown in Example 17, transcriptional activation ispossible. As also shown in Example 17, gene repression (in this case ofthe beta-catenin gene) is possible using a Cas9 repressor (DNA-bindingdomain) that binds to the target gene sequence, thus repressing itsactivity.

Cas9 and one or more guide RNA can be delivered using adeno associatedvirus (AAV), lentivirus, adenovirus or other plasmid or viral vectortypes, in particular, using formulations and doses from, for example,U.S. Pat. No. 8,454,972 (formulations, doses for adenovirus), U.S. Pat.No. 8,404,658 (formulations, doses for AAV) and U.S. Pat. No. 5,846,946(formulations, doses for DNA plasmids) and from clinical trials andpublications regarding the clinical trials involving lentivirus, AAV andadenovirus. For examples, for AAV, the route of administration,formulation and dose can be as in U.S. Pat. No. 8,454,972 and as inclinical trials involving AAV. For Adenovirus, the route ofadministration, formulation and dose can be as in U.S. Pat. No.8,404,658 and as in clinical trials involving adenovirus. For plasmiddelivery, the route of administration, formulation and dose can be as inU.S. Pat. No. 5,846,946 and as in clinical studies involving plasmids.Doses may be based on or extrapolated to an average 70 kg individual,and can be adjusted for patients, subjects, mammals of different weightand species. Frequency of administration is within the ambit of themedical or veterinary practitioner (e.g., physician, veterinarian),depending on usual factors including the age, sex, general health, otherconditions of the patient or subject and the particular condition orsymptoms being addressed.

The viral vectors can be injected into the tissue of interest. Forcell-type specific genome modification, the expression of Cas9 can bedriven by a cell-type specific promoter. For example, liver-specificexpression might use the Albumin promoter and neuron-specific expressionmight use the Synapsin I promoter.

Transgenic animals are also provided. Preferred examples include animalscomprising Cas9, in terms of polynucleotides encoding Cas9 or theprotein itself. Mice, rats and rabbits are preferred. To generatetransgenic mice with the constructs, as exemplified herein one mayinject pure, linear DNA into the pronucleus of a zygote from a pseudopregnant female, e.g. a CB56 female. Founders may then be identified,genotyped, and backcrossed to CB57 mice. The constructs may then becloned and optionally verified, for instance by Sanger sequencing. Knockouts are envisaged where for instance one or more genes are knocked outin a model. However, are knockins are also envisaged (alone or incombination). An example knockin Cas9 mouse was generated and this isexemplified, but Cas9 knockins are preferred. To generate a Cas9 knockin mice one may target the same constitutive and conditional constructsto the Rosa26 locus, as described herein (FIGS. 25A-B and 26). Methodsof US Patent Publication Nos. 20120017290 and 20110265198 assigned toSangamo BioSciences, Inc. directed to targeting the Rosa locus may bemodified to utilize the CRISPR Cas system of the present invention. Inanother embodiment, the methods of US Patent Publication No. 20130236946assigned to Cellectis directed to targeting the Rosa locus may also bemodified to utilize the CRISPR Cas system of the present invention.

Utility of the conditional Cas9 mouse: Applicants have shown in 293cells that the Cas9 conditional expression construct can be activated byco-expression with Cre. Applicants also show that the correctly targetedR1 mESCs can have active Cas9 when Cre is expressed. Because Cas9 isfollowed by the P2A peptide cleavage sequence and then EGFP Applicantsidentify successful expression by observing EGFP. Applicants have shownCas9 activation in mESCs. This same concept is what makes theconditional Cas9 mouse so useful. Applicants may cross their conditionalCas9 mouse with a mouse that ubiquitously expresses Cre (ACTB-Cre line)and may arrive at a mouse that expresses Cas9 in every cell. It shouldonly take the delivery of chimeric RNA to induce genome editing inembryonic or adult mice. Interestingly, if the conditional Cas9 mouse iscrossed with a mouse expressing Cre under a tissue specific promoter,there should only be Cas9 in the tissues that also express Cre. Thisapproach may be used to edit the genome in only precise tissues bydelivering chimeric RNA to the same tissue.

As mentioned above, transgenic animals are also provided, as aretransgenic plants, especially crops and algae. The transgenic plants maybe useful in applications outside of providing a disease model. Thesemay include food or feed production through expression of, for instance,higher protein, carbohydrate, nutrient or vitamin levels than wouldnormally be seen in the wildtype. In this regard, transgenic plants,especially pulses and tubers, and animals, especially mammals such aslivestock (cows, sheep, goats and pigs), but also poultry and edibleinsects, are preferred.

Transgenic algae or other plants such as rape may be particularly usefulin the production of vegetable oils or biofuels such as alcohols(especially methanol and ethanol), for instance. These may be engineeredto express or overexpress high levels of oil or alcohols for use in theoil or biofuel industries.

In terms of in vivo delivery, AAV is advantageous over other viralvectors for a couple of reasons:

Low toxicity (this may be due to the purification method not requiringultra centrifugation of cell particles that can activate the immuneresponse)

Low probability of causing insertional mutagenesis because it doesn'tintegrate into the host genome.

AAV has a packaging limit of 4.5 or 4.75 Kb. This means that Cas9 aswell as a promoter and transcription terminator have to be all fit intothe same viral vector. Constructs larger than 4.5 or 4.75 Kb will leadto significantly reduced virus production. SpCas9 is quite large, thegene itself is over 4.1 Kb, which makes it difficult for packing intoAAV. Therefore embodiments of the invention include utilizing homologsof Cas9 that are shorter. For example:

Species Cas9 Size Corynebacter diphtheriae 3252 Eubacterium ventriosum3321 Streptococcus pasteurianus 3390 Lactobacillus farciminis 3378Sphaerochaeta globus 3537 Azospirillum B510 3504 Gluconacetobacterdiazotrophicus 3150 Neisseria cinerea 3246 Roseburia intestinalis 3420Parvibaculum lavamentivorans 3111 Staphylococcus aureus 3159Nitratifractor salsuginis DSM 16511 3396 Campylobacter lari CF89-12 3009Streptococcus thermophilus LMD-9 3396

These species are therefore, in general, preferred Cas9 species.Applicants have shown delivery and in vivo mouse brain Cas9 expressiondata.

Two ways to package Cas9 coding nucleic acid molecules, e.g., DNA, intoviral vectors to mediate genome modification in vivo are preferred:

To achieve NHEJ-mediated gene knockout:

Single virus vector:

Vector containing two or more expression cassettes:

Promoter-Cas9 coding nucleic acid molecule-terminator

Promoter-gRNA1-terminator

Promoter-gRNA2-terminator

Promoter-gRNA(N)-terminator (up to size limit of vector)

Double virus vector:

Vector 1 containing one expression cassette for driving the expressionof Cas9

Promoter-Cas9 coding nucleic acid molecule-terminator

Vector 2 containing one more expression cassettes for driving theexpression of one or more guideRNAs

Promoter-gRNA 1-terminator

Promoter-gRNA(N)-terminator (up to size limit of vector)

To mediate homology-directed repair. In addition to the single anddouble virus vector approaches described above, an additional vector isused to deliver a homology-direct repair template.

Promoter used to drive Cas9 coding nucleic acid molecule expression caninclude:

AAV ITR can serve as a promoter: this is advantageous for eliminatingthe need for an additional promoter element (which can take up space inthe vector). The additional space freed up can be used to drive theexpression of additional elements (gRNA, etc.). Also, ITR activity isrelatively weaker, so can be used to reduce toxicity due to overexpression of Cas9.

For ubiquitous expression, can use promoters: CMV, CAG, CBh, PGK, SV40,Ferritin heavy or light chains, etc.

For brain expression, can use promoters: SynapsinI for all neurons,CaMKIIalpha for excitatory neurons, GAD67 or GAD65 or VGAT for GABAergicneurons, etc.

For liver expression, can use Albumin promoter.

For lung expression, can use SP-B.

For endothelial cells, can use ICAM.

For hematopoietic cells can use IFNbeta or CD45.

For Osteoblasts can use OG-2.

Promoter used to drive guide RNA can include:

Pol III promoters such as U6 or H1

Use of Pol II promoter and intronic cassettes to express gRNA

As to AAV, the AAV can be AAV1, AAV2, AAV5 or any combination thereof.One can select the AAV of the AAV with regard to the cells to betargeted; e.g., one can select AAV serotypes 1, 2, 5 or a hybrid orcapsid AAV1, AAV2, AAV5 or any combination thereof for targeting brainor neuronal cells; and one can select AAV4 for targeting cardiac tissue.AAV8 is useful for delivery to the liver. The above promoters andvectors are preferred individually.

RNA delivery is also a useful method of in vivo delivery. FIG. 27 showsdelivery and in vivo mouse brain Cas9 expression data. It is possible todeliver Cas9 and gRNA (and, for instance, HR repair template) into cellsusing liposomes or nanoparticles. Thus delivery of the CRISPR enzyme,such as a Cas9 and/or delivery of the RNAs of the invention may be inRNA form and via microvesicles, liposomes or nanoparticles. For example,Cas9 mRNA and gRNA can be packaged into liposomal particles for deliveryin vivo. Liposomal transfection reagents such as lipofectamine from LifeTechnologies and other reagents on the market can effectively deliverRNA molecules into the liver.

Enhancing NHEJ or HR efficiency is also helpful for delivery. It ispreferred that NHEJ efficiency is enhanced by co-expressingend-processing enzymes such as Trex2 (Dumitrache et al. Genetics. 2011August; 188(4): 787-797). It is preferred that HR efficiency isincreased by transiently inhibiting NHEJ machineries such as Ku70 andKu86. HR efficiency can also be increased by co-expressing prokaryoticor eukaryotic homologous recombination enzymes such as RecBCD, RecA.

Various means of delivery are described herein, and further discussed inthis section.

Viral delivery: The CRISPR enzyme, for instance a Cas9, and/or any ofthe present RNAs, for instance a guide RNA, can be delivered using adenoassociated virus (AAV), lentivirus, adenovirus or other viral vectortypes, or combinations thereof. Cas9 and one or more guide RNAs can bepackaged into one or more viral vectors. In some embodiments, the viralvector is delivered to the tissue of interest by, for example, anintramuscular injection, while other times the viral delivery is viaintravenous, transdermal, intranasal, oral, mucosal, or other deliverymethods. Such delivery may be either via a single dose, or multipledoses. One skilled in the art understands that the actual dosage to bedelivered herein may vary greatly depending upon a variety of factors,such as the vector chose, the target cell, organism, or tissue, thegeneral condition of the subject to be treated, the degree oftransformation/modification sought, the administration route, theadministration mode, the type of transformation/modification sought,etc.

Such a dosage may further contain, for example, a carrier (water,saline, ethanol, glycerol, lactose, sucrose, calcium phosphate, gelatin,dextran, agar, pectin, peanut oil, sesame oil, etc.), a diluent, apharmaceutically-acceptable carrier (e.g., phosphate-buffered saline), apharmaceutically-acceptable excipient, an adjuvant to enhanceantigenicity, an immunostimulatory compound or molecule, and/or othercompounds known in the art. The adjuvant herein may contain a suspensionof minerals (alum, aluminum hydroxide, aluminum phosphate) on whichantigen is adsorbed; or water-in-oil emulsion in which antigen solutionis emulsified in oil (MF-59, Freund's incomplete adjuvant), sometimeswith the inclusion of killed mycobacteria (Freund's complete adjuvant)to further enhance antigenicity (inhibits degradation of antigen and/orcauses influx of macrophages). Adjuvants also include immunostimulatorymolecules, such as cytokines, costimulatory molecules, and for example,immunostimulatory DNA or RNA molecules, such as CpG oligonucleotides.Such a dosage formulation is readily ascertainable by one skilled in theart. The dosage may further contain one or more pharmaceuticallyacceptable salts such as, for example, a mineral acid salt such as ahydrochloride, a hydrobromide, a phosphate, a sulfate, etc.; and thesalts of organic acids such as acetates, propionates, malonates,benzoates, etc. Additionally, auxiliary substances, such as wetting oremulsifying agents, pH buffering substances, gels or gelling materials,flavorings, colorants, microspheres, polymers, suspension agents, etc.may also be present herein. In addition, one or more other conventionalpharmaceutical ingredients, such as preservatives, humectants,suspending agents, surfactants, antioxidants, anticaking agents,fillers, chelating agents, coating agents, chemical stabilizers, etc.may also be present, especially if the dosage form is a reconstitutableform. Suitable exemplary ingredients include microcrystalline cellulose,carboxymethylcellulose sodium, polysorbate 80, phenylethyl alcohol,chlorobutanol, potassium sorbate, sorbic acid, sulfur dioxide, propylgallate, the parabens, ethyl vanillin, glycerin, phenol,parachlorophenol, gelatin, albumin and a combination thereof. A thoroughdiscussion of pharmaceutically acceptable excipients is available inREMINGTON'S PHARMACEUTICAL SCIENCES (Mack Pub. Co., N.J. 1991) which isincorporated by reference herein.

In an embodiment herein the delivery is via an adenovirus, which may beat a single booster dose containing at least 1×10⁵ particles (alsoreferred to as particle units, pu) of adenoviral vector. In anembodiment herein, the dose preferably is at least about 1×10⁶ particles(for example, about 1×10⁶-1×10¹² particles), more preferably at leastabout 1×10⁷ particles, more preferably at least about 1×10⁸ particles(e.g., about 1×10⁸-1×10¹¹ particles or about 1×10⁸-1×10¹² particles),and most preferably at least about 1×10⁰ particles (e.g., about1×10⁹-1×10¹⁰ particles or about 1×10⁹-×10¹² particles), or even at leastabout 1×10¹⁰ particles (e.g., about 1×10¹⁰-1×10¹² particles) of theadenoviral vector. Alternatively, the dose comprises no more than about1×10¹⁴ particles, preferably no more than about 1×10¹³ particles, evenmore preferably no more than about 1×10¹² particles, even morepreferably no more than about 1×10¹¹ particles, and most preferably nomore than about 1×10¹⁰ particles (e.g., no more than about 1×10⁹articles). Thus, the dose may contain a single dose of adenoviral vectorwith, for example, about 1×10⁶ particle units (pu), about 2×10⁶ pu,about 4×10⁶ pu, about 1×10⁷ pu, about 2×10⁷ pu, about 4×10⁷ pu, about1×10⁸ pu, about 2×10⁸ pu, about 4×10⁸ pu, about 1×10⁹ pu, about 2×10⁹pu, about 4×10⁹ pu, about 1×10¹⁰ pu, about 2×10¹⁰ pu, about 4×10¹⁰ pu,about 1×10¹¹ pu, about 2×10¹¹ pu, about 4×10¹¹ pu, about 1×10¹² pu,about 2×10¹² pu, or about 4×10¹² pu of adenoviral vector. See, forexample, the adenoviral vectors in U.S. Pat. No. 8,454,972 B2 to Nabel,et. al., granted on Jun. 4, 2013; incorporated by reference herein, andthe dosages at col 29, lines 36-58 thereof. In an embodiment herein, theadenovirus is delivered via multiple doses.

In an embodiment herein, the delivery is via an AAV. A therapeuticallyeffective dosage for in vivo delivery of the AAV to a human is believedto be in the range of from about 20 to about 50 ml of saline solutioncontaining from about 1×10¹⁰ to about 1×10¹⁰ functional AAV/ml solution.The dosage may be adjusted to balance the therapeutic benefit againstany side effects. In an embodiment herein, the AAV dose is generally inthe range of concentrations of from about 1×10⁵ to 1×10⁵⁰ genomes AAV,from about 1×10⁸ to 1×10²⁰ genomes AAV, from about 1×10¹⁰ to about1×10¹⁶ genomes, or about 1×10¹¹ to about 1×10¹⁶ genomes AAV. A humandosage may be about 1×10¹³ genomes AAV. Such concentrations may bedelivered in from about 0.001 ml to about 100 ml, about 0.05 to about 50ml, or about 10 to about 25 ml of a carrier solution. Other effectivedosages can be readily established by one of ordinary skill in the artthrough routine trials establishing dose response curves. See, forexample, U.S. Pat. No. 8,404,658 B2 to Hajjar, et al., granted on Mar.26, 2013, at col. 27, lines 45-60.

In an embodiment herein the delivery is via a plasmid. In such plasmidcompositions, the dosage should be a sufficient amount of plasmid toelicit a response. For instance, suitable quantities of plasmid DNA inplasmid compositions can be from about 0.1 to about 2 mg, or from about1 μg to about 10 μg.

The doses herein are based on an average 70 kg individual. The frequencyof administration is within the ambit of the medical or veterinarypractitioner (e.g., physician, veterinarian), or scientist skilled inthe art.

Lentiviruses are complex retroviruses that have the ability to infectand express their genes in both mitotic and post-mitotic cells. The mostcommonly known lentivirus is the human immunodeficiency virus (HIV),which uses the envelope glycoproteins of other viruses to target a broadrange of cell types.

Lentiviruses may be prepared as follows. After cloning pCasES10 (whichcontains a lentiviral transfer plasmid backbone), HEK293FT at lowpassage (p=5) were seeded in a T-75 flask to 50% confluence the daybefore transfection in DMEM with 10% fetal bovine serum and withoutantibiotics. After 20 hours, media was changed to OptiMEM (serum-free)media and transfection was done 4 hours later. Cells were transfectedwith 10 μg of lentiviral transfer plasmid (pCasES10) and the followingpackaging plasmids: 5 μg of pMD2.G (VSV-g pseudotype), and 7.5 μg ofpsPAX2 (gag/pol/rev/tat). Transfection was done in 4 mL OptiMEM with acationic lipid delivery agent (50 uL Lipofectamine 2000 and 100 ul Plusreagent). After 6 hours, the media was changed to antibiotic-free DMEMwith 10% fetal bovine serum.

Lentivirus may be purified as follows. Viral supernatants were harvestedafter 48 hours. Supernatants were first cleared of debris and filteredthrough a 0.45 um low protein binding (PVDF) filter. They were then spunin a ultracentrifuge for 2 hours at 24,000 rpm. Viral pellets wereresuspended in 50 ul of DMEM overnight at 4 C. They were then aliquottedand immediately frozen at −80 C.

In another embodiment, minimal non-primate lentiviral vectors based onthe equine infectious anemia virus (EIAV) are also contemplated,especially for ocular gene therapy (see, e.g., Balagaan, J Gene Med2006; 8: 275-285, Published online 21 Nov. 2005 in Wiley InterScience(www.interscience.wiley.com). DOI: 10.1002/jgm.845). In anotherembodiment, RetinoStat®, an equine infectious anemia virus-basedlentiviral gene therapy vector that expresses angiostatic proteinsendostain and angiostatin that is delivered via a subretinal injectionfor the treatment of the web form of age-related macular degeneration isalso contemplated (see, e.g., Binley et al., HUMAN GENE THERAPY23:980-991 (September 2012)) may be modified for the CRISPR-Cas systemof the present invention.

In another embodiment, self-inactivating lentiviral vectors with ansiRNA targeting a common exon shared by HIV tat/rev, anucleolar-localizing TAR decoy, and an anti-CCR5-specific hammerheadribozyme (see, e.g., DiGiusto et al. (2010) Sci Transl Med 2:36ra43) maybe used/and or adapted to the CRISPR-Cas system of the presentinvention. A minimum of 2.5×10⁶ CD34+ cells per kilogram patient weightmay be collected and prestimulated for 16 to 20 hours in X-VIVO 15medium (Lonza) containing 2 mML-glutamine, stem cell factor (100 ng/ml),Flt-3 ligand (Flt-3L) (100 ng/ml), and thrombopoietin (10 ng/ml)(CellGenix) at a density of 2×10⁶ cells/ml. Prestimulated cells may betransduced with lentiviral at a multiplicity of infection of 5 for 16 to24 hours in 75-cm² tissue culture flasks coated with fibronectin (25mg/cm²) (RetroNectin, Takara Bio Inc.).

Lentiviral vectors have been disclosed as in the treatment forParkinson's Disease, see, e.g., US Patent Publication No. 20120295960and U.S. Pat. Nos. 7,303,910 and 7,351,585. Lentiviral vectors have alsobeen disclosed for the treatment of ocular diseases, see e.g., US PatentPublication Nos. 20060281180, 20090007284, US20110117189; US20090017543;US20070054961, US20100317109. Lentiviral vectors have also beendisclosed for delivery to the train, see, e.g., US Patent PublicationNos. US20110293571; US20110293571, US20040013648, US20070025970,US20090111106 and U.S. Pat. No. 7,259,015.

RNA delivery: The CRISPR enzyme, for instance a Cas9, and/or any of thepresent RNAs, for instance a guide RNA, can also be delivered in theform of RNA. Cas9 mRNA can be generated using in vitro transcription.For example, Cas9 mRNA can be synthesized using a PCR cassettecontaining the following elements: T7_promoter-kozak sequence(GCCACC)-Cas9-3′ UTR from beta globin-polyA tail (a string of 120 ormore adenines). The cassette can be used for transcription by T7polymerase. Guide RNAs can also be transcribed using in vitrotranscription from a cassette containing T7_promoter-GG-guide RNAsequence.

To enhance expression and reduce toxicity, the CRISPR enzyme and/orguide RNA can be modified using pseudo-U or 5-Methyl-C.

mRNA delivery methods are especially promising for liver deliverycurrently. In particular, for AAV8 is particularly preferred fordelivery to the liver.

CRISPR enzyme mRNA and guide RNA might also be delivered separately.CRISPR enzyme mRNA can be delivered prior to the guide RNA to give timefor CRISPR enzyme to be expressed. CRISPR enzyme mRNA might beadministered 1-12 hours (preferably around 2-6 hours) prior to theadministration of guide RNA.

Alternatively, CRISPR enzyme mRNA and guide RNA can be administeredtogether. Advantageously, a second booster dose of guide RNA can beadministered 1-12 hours (preferably around 2-6 hours) after the initialadministration of CRISPR enzyme mRNA+guide RNA.

Additional administrations of CRISPR enzyme mRNA and/or guide RNA mightbe useful to achieve the most efficient levels of genome modification.

For minimization of toxicity and off-target effect, it will be importantto control the concentration of CRISPR enzyme mRNA and guide RNAdelivered. Optimal concentrations of CRISPR enzyme mRNA and guide RNAcan be determined by testing different concentrations in a cellular oranimal model and using deep sequencing the analyze the extent ofmodification at potential off-target genomic loci. For example, for theguide sequence targeting 5′-GAGTCCGAGCAGAAGAAGAA-3′ in the EMX1 gene ofthe human genome, deep sequencing can be used to assess the level ofmodification at the following two off-target loci, 1:5′-GAGTCCTAGCAGGAGAAGAA-3′ and 2: 5′-GAGTCTAAGCAGAAGAAGAA-3′. Theconcentration that gives the highest level of on-target modificationwhile minimizing the level of off-target modification should be chosenfor in vivo delivery.

Alternatively, to minimize the level of toxicity and off-target effect,CRISPR enzyme nickase mRNA (for example S. pyogenes Cas9 with the D10Amutation) can be delivered with a pair of guide RNAs targeting a site ofinterest. The two guide RNAs need to be spaced as follows. Guidesequences in red (single underline) and blue (double underline)respectively (these examples are based on the PAM requirement forStreptococcus pyogenes Cas9).

Overhang length (bp)Guide RNA design (guide sequence and PAM color coded) 145′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNN-5′ 135′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNN-5′ 125′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNN-5′ 115′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNN-5′ 105′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNN-5′  95′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNN-5′  85′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNN-5′  75′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNN-5′  65′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNCCNNNNN NNNNNNNNNNNNNNNNN-5′  55′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNN-5′  45′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNNN-5′  35′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNNNNN-5′  25′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNNNNN-5′  15′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNNNNNN-5′ blunt 5′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5′  15′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNCCNNNNNNNNNNNN NNNNNNNNNNNNNNNNN-5′  25′-NNNNNNNNNNNNNNNNNNNNCCNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNNCC NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5′  35′-NNNNNNNNNNNNNNNNNNNNCCNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5′  45′-NNNNNNNNNNNNNNNNNNNNCCNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNNCCNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNN-5′  55′-NNNNNNNNNNNNNNNNNNNNCCNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5′  65′-NNNNNNNNNNNNNNNNNNNNCCNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5′  75′-NNNNNNNNNNNNNNNNNNNNCCNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNGGNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5′  85′-NNNNNNNNNNNNNNNNNNNNNCCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNNGGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5′ 125′-NNNNNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNNNNCCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5′ 135′-NNNNNNNNNNNNNNNNNNNNNNCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNNNNCCNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5′ 145′-NNNNNNNNNNNNNNNNNNNNNNCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNNNNCCNNGGNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNN-5′ 155′-NNNNNNNNNNNNNNNNNNNNNNCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNNNNCCNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5′ 165′-NNNNNNNNNNNNNNNNNNNNNNCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNNNCCNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5′ 175′-NNNNNNNNNNNNNNNNNNNNNNCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′3′-NNNNNNNNNNNNNNNNNNNNNNNCCNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5′

Further interrogation of the system have given Applicants evidence ofthe 5′overhang (see, e.g., Ran et al., Cell. 2013 Sep. 12; 154(6):1380-9and U.S. Provisional Patent Application Ser. No. 61/871,301 filed Aug.28, 2013). Applicants have further identified parameters that relate toefficient cleavage by the Cas9 nickase mutant when combined with twoguide RNAs and these parameters include but are not limited to thelength of the 5′ overhang. In embodiments of the invention the 5′overhang is at most 200 base pairs, preferably at most 100 base pairs,or more preferably at most 50 base pairs. In embodiments of theinvention the 5′ overhang is at least 26 base pairs, preferably at least30 base pairs or more preferably 34-50 base pairs or 1-34 base pairs. Inother preferred methods of the invention the first guide sequencedirecting cleavage of one strand of the DNA duplex near the first targetsequence and the second guide sequence directing cleavage of otherstrand near the second target sequence results in a blunt cut or a 3′overhang. In embodiments of the invention the 3′ overhang is at most150, 100 or 25 base pairs or at least 15, 10 or 1 base pairs. Inpreferred embodiments the 3′ overhang is 1-100 basepairs.

Aspects of the invention relate to the expression of the gene productbeing decreased or a template polynucleotide being further introducedinto the DNA molecule encoding the gene product or an interveningsequence being excised precisely by allowing the two 5′ overhangs toreanneal and ligate or the activity or function of the gene productbeing altered or the expression of the gene product being increased. Inan embodiment of the invention, the gene product is a protein.

Only sgRNA pairs creating 5′ overhangs with less than 8 bp overlapbetween the guide sequences (offset greater than −8 bp) were able tomediate detectable indel formation. Importantly, each guide used inthese assays is able to efficiently induce indels when paired withwildtype Cas9, indicating that the relative positions of the guide pairsare the most important parameters in predicting double nicking activity.

Since Cas9n and Cas9H840A nick opposite strands of DNA, substitution ofCas9n with Cas9H840A with a given sgRNA pair should result in theinversion of the overhang type. For example, a pair of sgRNAs that willgenerate a 5′ overhang with Cas9n should in principle generate thecorresponding 3′ overhang instead. Therefore, sgRNA pairs that lead tothe generation of a 3′ overhang with Cas9n might be used with Cas9H840Ato generate a 5′ overhang. Unexpectedly, Applicants tested Cas9H840Awith a set of sgRNA pairs designed to generate both 5′ and 3′ overhangs(offset range from −278 to +58 bp), but were unable to observe indelformation. Further work may be needed to identify the necessary designrules for sgRNA pairing to allow double nicking by Cas9H840A.

Targeted deletion of genes is preferred. Examples are exemplified inExample 18. Preferred are, therefore, genes involved in cholesterolbiosynthesis, fatty acid biosynthesis, and other metabolic disorders,genes encoding mis-folded proteins involved in amyloid and otherdiseases, oncogenes leading to cellular transformation, latent viralgenes, and genes leading to dominant-negative disorders, amongst otherdisorders. As exemplified here, Applicants prefer gene delivery of aCRISPR-Cas system to the liver, brain, ocular, epithelial, hematopoetic,or another tissue of a subject or a patient in need thereof, sufferingfrom metabolic disorders, amyloidosis and protein-aggregation relateddiseases, cellular transformation arising from genetic mutations andtranslocations, dominant negative effects of gene mutations, latentviral infections, and other related symptoms, using either viral ornanoparticle delivery system.

Therapeutic applications of the CRISPR-Cas system include Glaucoma,Amyloidosis, and Huntington's disease. These are exemplified in Example20 and the features described therein are preferred alone or incombination.

Another example of a polyglutamine expansion disease that may be treatedby the present invention includes spinocerebellar ataxia type 1 (SCA1).Upon intracerebellar injection, recombinant adenoassociated virus (AAV)vectors expressing short hairpin RNAs profoundly improve motorcoordination, restored cerebellar morphology and resolved characteristicataxin-inclusions in Purkinje cells of SCA1 mice (see, e.g., Xia et al.,Nature Medicine. Vol. 10, No. 8, August 2004). In particular, AAV1 andAAV5 vectors are preferred and AAV titers of about 1×10¹² vectorgenomes/ml are desirable.

As an example, chronic infection by HIV-1 may be treated or prevented.In order to accomplish this, one may generate CRISPR-Cas guide RNAs thattarget the vast majority of the HIV-1 genome while taking into accountHIV-1 strain variants for maximal coverage and effectiveness. One mayaccomplish delivery of the CRISPR-Cas system by conventional adenoviralor lentiviral-mediated infection of the host immune system. Depending onapproach, host immune cells could be a) isolated, transduced withCRISPR-Cas, selected, and re-introduced in to the host or b) transducedin vivo by systemic delivery of the CRISPR-Cas system. The firstapproach allows for generation of a resistant immune population whereasthe second is more likely to target latent viral reservoirs within thehost. This is discussed in more detail in the Examples section.

In another example, US Patent Publication No. 20130171732 assigned toSangamo BioSciences, Inc. relates to insertion of an anti-HIV transgeneinto the genome, methods of which may be applied to the CRISPR Cassystem of the present invention. In another embodiment, the CXCR4 genemay be targeted and the TALE system of US Patent Publication No.20100291048 assigned to Sangamo BioSciences, Inc. may be modified to theCRISPR Cas system of the present invention. The method of US PatentPublication Nos. 20130137104 and 20130122591 assigned to SangamoBioSciences, Inc. and US Patent Publication No. 20100146651 assigned toCellectis may be more generally applicable for transgene expression asit involves modifying a hypoxanthine-guanine phosphoribosyltransferase(HPRT) locus for increasing the frequency of gene modification.

It is also envisaged that the present invention generates a geneknockout cell library. Each cell may have a single gene knocked out.This is exemplified in Example 23.

One may make a library of ES cells where each cell has a single geneknocked out, and the entire library of ES cells will have every singlegene knocked out. This library is useful for the screening of genefunction in cellular processes as well as diseases. To make this celllibrary, one may integrate Cas9 driven by an inducible promoter (e.g.doxycycline inducible promoter) into the ES cell. In addition, one mayintegrate a single guide RNA targeting a specific gene in the ES cell.To make the ES cell library, one may simply mix ES cells with a libraryof genes encoding guide RNAs targeting each gene in the human genome.One may first introduce a single BxB1 attB site into the AAVS1 locus ofthe human ES cell. Then one may use the BxB1 integrase to facilitate theintegration of individual guide RNA genes into the BxB1 attB site inAAVS1 locus. To facilitate integration, each guide RNA gene may becontained on a plasmid that carries of a single attP site. This way BxB1will recombine the attB site in the genome with the attP site on theguide RNA containing plasmid. To generate the cell library, one may takethe library of cells that have single guide RNAs integrated and induceCas9 expression. After induction, Cas9 mediates double strand break atsites specified by the guide RNA.

Chronic administration of protein therapeutics may elicit unacceptableimmune responses to the specific protein. The immunogenicity of proteindrugs can be ascribed to a few immunodominant helper T lymphocyte (HTL)epitopes. Reducing the MHC binding affinity of these HTL epitopescontained within these proteins can generate drugs with lowerimmunogenicity (Tangri S, et al. (“Rationally engineered therapeuticproteins with reduced immunogenicity” J Immunol. 2005 Mar. 15;174(6):3187-96.) In the present invention, the immunogenicity of theCRISPR enzyme in particular may be reduced following the approach firstset out in Tangri et al with respect to erythropoietin and subsequentlydeveloped. Accordingly, directed evolution or rational design may beused to reduce the immunogenicity of the CRISPR enzyme (for instance aCas9) in the host species (human or other species).

In Example 28, Applicants used 3 guideRNAs of interest and able tovisualize efficient DNA cleavage in vivo occurring only in a smallsubset of cells. Essentially, what Applicants have shown here istargeted in vivo cleavage. In particular, this provides proof of conceptthat specific targeting in higher organisms such as mammals can also beachieved. It also highlights multiplex aspect in that multiple guidesequences (i.e. separate targets) can be used simultaneously (in thesense of co-delivery). In other words, Applicants used a multipleapproach, with several different sequences targeted at the same time,but independently.

A suitable example of a protocol for producing AAV, a preferred vectorof the invention is provided in Example 34.

Trinucleotide repeat disorders are preferred conditions to be treated.These are also exemplified herein.

For example, US Patent Publication No. 20110016540, describes use ofzinc finger nucleases to genetically modify cells, animals and proteinsassociated with trinucleotide repeat expansion disorders. Trinucleotiderepeat expansion disorders are complex, progressive disorders thatinvolve developmental neurobiology and often affect cognition as well assensori-motor functions.

Trinucleotide repeat expansion proteins are a diverse set of proteinsassociated with susceptibility for developing a trinucleotide repeatexpansion disorder, the presence of a trinucleotide repeat expansiondisorder, the severity of a trinucleotide repeat expansion disorder orany combination thereof. Trinucleotide repeat expansion disorders aredivided into two categories determined by the type of repeat. The mostcommon repeat is the triplet CAG, which, when present in the codingregion of a gene, codes for the amino acid glutamine (Q). Therefore,these disorders are referred to as the polyglutamine (polyQ) disordersand comprise the following diseases: Huntington Disease (HD);Spinobulbar Muscular Atrophy (SBMA); Spinocerebellar Ataxias (SCA types1, 2, 3, 6, 7, and 17); and Dentatorubro-Pallidoluysian Atrophy (DRPLA).The remaining trinucleotide repeat expansion disorders either do notinvolve the CAG triplet or the CAG triplet is not in the coding regionof the gene and are, therefore, referred to as the non-polyglutaminedisorders. The non-polyglutamine disorders comprise Fragile X Syndrome(FRAXA); Fragile XE Mental Retardation (FRAXE); Friedreich Ataxia(FRDA); Myotonic Dystrophy (DM); and Spinocerebellar Ataxias (SCA types8, and 12).

The proteins associated with trinucleotide repeat expansion disordersare typically selected based on an experimental association of theprotein associated with a trinucleotide repeat expansion disorder to atrinucleotide repeat expansion disorder. For example, the productionrate or circulating concentration of a protein associated with atrinucleotide repeat expansion disorder may be elevated or depressed ina population having a trinucleotide repeat expansion disorder relativeto a population lacking the trinucleotide repeat expansion disorder.Differences in protein levels may be assessed using proteomic techniquesincluding but not limited to Western blot, immunohistochemical staining,enzyme linked immunosorbent assay (ELISA), and mass spectrometry.Alternatively, the proteins associated with trinucleotide repeatexpansion disorders may be identified by obtaining gene expressionprofiles of the genes encoding the proteins using genomic techniquesincluding but not limited to DNA microarray analysis, serial analysis ofgene expression (SAGE), and quantitative real-time polymerase chainreaction (Q-PCR).

Non-limiting examples of proteins associated with trinucleotide repeatexpansion disorders include AR (androgen receptor), FMR1 (fragile Xmental retardation 1), HTT (huntingtin), DMPK (dystrophiamyotonica-protein kinase), FXN (frataxin), ATXN2 (ataxin 2), ATN1(atrophin 1), FEN1 (flap structure-specific endonuclease 1), TNRC6A(trinucleotide repeat containing 6A), PABPN1 (poly(A) binding protein,nuclear 1), JPH3 (junctophilin 3), MED15 (mediator complex subunit 15),ATXN1 (ataxin 1), ATXN3 (ataxin 3), TBP (TATA box binding protein),CACNA1A (calcium channel, voltage-dependent, P/Q type, alpha 1Asubunit), ATXN80S (ATXN8 opposite strand (non-protein coding)), PPP2R2B(protein phosphatase 2, regulatory subunit B, beta), ATXN7 (ataxin 7),TNRC6B (trinucleotide repeat containing 6B), TNRC6C (trinucleotiderepeat containing 6C), CELF3 (CUGBP, Elav-like family member 3), MAB21L1(mab-21-like 1 (C. elegans)), MSH2 (mutS homolog 2, colon cancer,nonpolyposis type I (E. coli)). TMEM185A (transmembrane protein 185A),SIX5 (SIX homeobox 5). CNPY3 (canopy 3 homolog (zebrafish)), FRAXE(fragile site, folic acid type, rare, fra(X)q28) E), GNB2 (guaninenucleotide binding protein (G protein), beta polypeptide 2), RPL14(ribosomal protein L14), ATXN8 (ataxin 8), INSR (insulin receptor), TTR(transthyretin), EP400 (E1A binding protein p400), GIGYF2 (GRB10interacting GYF protein 2), OGG1 (8-oxoguanine DNA glycosylase). STC1(stanniocalcin 1), CNDP1 (carnosine dipeptidase 1 (metallopeptidase M20family)), C10orf2 (chromosome 10 open reading frame 2), MAML3mastermind-like 3 (Drosophila), DKC1 (dyskeratosis congenita 1,dyskerin), PAXIP1 (PAX interacting (with transcription-activationdomain) protein 1), CASK (calcium/calmodulin-dependent serine proteinkinase (MAGUK family)), MAPT (microtubule-associated protein tau), SP1(Sp1 transcription factor), POLG (polymerase (DNA directed), gamma),AFF2 (AF4/FMR2 family, member 2), THBS1 (thrombospondin 1), TP53 (tumorprotein p53), ESR1 (estrogen receptor 1), CGGBP1 (CGG triplet repeatbinding protein 1), ABT1 (activator of basal transcription 1), KLK3(kallikrein-related peptidase 3), PRNP (prion protein), JUN (junoncogene), KCNN3 (potassium intermediate/small conductancecalcium-activated channel, subfamily N, member 3), BAX (BCL2-associatedX protein), FRAXA (fragile site, folic acid type, rare, fra(X)(q27.3) A(macroorchidism, mental retardation)). KBTBD10 (kelch repeat and BTB(POZ) domain containing 10), MBNL1 (muscleblind-like (Drosophila)),RAD51 (RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae)), NCOA3(nuclear receptor coactivator 3), ERDA1 (expanded repeat domain, CAG/CTG1), TSC1 (tuberous sclerosis 1), COMP (cartilage oligomeric matrixprotein), GCLC (glutamate-cysteine ligase, catalytic subunit), RRAD(Ras-related associated with diabetes). MSH3 (mutS homolog 3 (E. coli)),DRD2 (dopamine receptor D2), CD44 (CD44 molecule (Indian blood group)),CTCF (CCCTC-binding factor (zinc finger protein)), CCND1 (cyclin D1),CLSPN (claspin homolog (Xenopus laevis)), MEF2A (myocyte enhancer factor2A), PTPRU (protein tyrosine phosphatase, receptor type, U), GAPDH(glyceraldehyde-3-phosphate dehydrogenase), TRIM22 (tripartitemotif-containing 22), WT1 (Wilms tumor 1), AHR (aryl hydrocarbonreceptor), GPX1 (glutathione peroxidase 1), TPMT (thiopurineS-methyltransferase), NDP (Norrie disease (pseudoglioma)), ARX(aristaless related homeobox), MUS81 (MUS81 endonuclease homolog (S.cerevisiae)), TYR (tyrosinase (oculocutaneous albinism IA)), EGR1 (earlygrowth response 1), UNG (uracil-DNA glycosylase). NUMBL (numb homolog(Drosophila)-like), FABP2 (fatty acid binding protein 2, intestinal),EN2 (engrailed homeobox 2), CRYGC (crystallin, gamma C). SRP14 (signalrecognition particle 14 kDa (homologous Alu RNA binding protein)), CRYGB(crystallin, gamma B), PDCD1 (programmed cell death 1), HOXA1 (homeoboxA1), ATXN2L (ataxin 2-like), PMS2 (PMS2 postmeiotic segregationincreased 2 (S. cerevisiae)), GLA (galactosidase, alpha), CBL (Cas-Br-M(murine) ecotropic retroviral transforming sequence), FTH1 (ferritin,heavy polypeptide 1), IL12RB2 (interleukin 12 receptor, beta 2), OTX2(orthodenticle homeobox 2), HOXA5 (homeobox A5), POLG2 (polymerase (DNAdirected), gamma 2, accessory subunit), DLX2 (distal-less homeobox 2),SIRPA (signal-regulatory protein alpha). OTX1 (orthodenticle homeobox1), AHRR (aryl-hydrocarbon receptor repressor), MANF (mesencephalicastrocyte-derived neurotrophic factor), TMEM158 (transmembrane protein158 (gene/pseudogene)), and ENSG00000078687.

Preferred proteins associated with trinucleotide repeat expansiondisorders include HTT (Huntingtin), AR (androgen receptor), FXN(frataxin), Atxn3 (ataxin), Atxn1 (ataxin), Atxn2 (ataxin), Atxn7(ataxin), Atxn10 (ataxin), DMPK (dystrophia myotonica-protein kinase),Atn1 (atrophin 1), CBP (creb binding protein), VLDLR (very low densitylipoprotein receptor), and any combination thereof.

According to another aspect, a method of gene therapy for the treatmentof a subject having a mutation in the CFTR gene is provided andcomprises administering a therapeutically effective amount of aCRISPR-Cas gene therapy particle, optionally via a biocompatiblepharmaceutical carrier, to the cells of a subject. Preferably, thetarget DNA comprises the mutation deltaF508. In general, it is ofpreferred that the mutation is repaired to the wildtype. In this case,the mutation is a deletion of the three nucleotides that comprise thecodon for phenylalanine (F) at position 508. Accordingly, repair in thisinstance requires reintroduction of the missing codon into the mutant.

To implement this Gene Repair Strategy, it is preferred that anadenovirus/AAV vector system is introduced into the host cell, cells orpatient. Preferably, the system comprises a Cas9 (or Cas9 nickase) andthe guide RNA along with a adenovirus/AAV vector system comprising thehomology repair template containing the F508 residue. This may beintroduced into the subject via one of the methods of delivery discussedearlier. The CRISPR-Cas system may be guided by the CFTRdelta 508chimeric guide RNA. It targets a specific site of the CFTR genomic locusto be nicked or cleaved. After cleavage, the repair template is insertedinto the cleavage site via homologous recombination correcting thedeletion that results in cystic fibrosis or causes cystic fibrosisrelated symptoms. This strategy to direct delivery and provide systemicintroduction of CRISPR systems with appropriate guide RNAs can beemployed to target genetic mutations to edit or otherwise manipulategenes that cause metabolic, liver, kidney and protein diseases anddisorders such as those in Table B.

The CRISPR/Cas9 systems of the present invention can be used to correctgenetic mutations that were previously attempted with limited successusing TALEN and ZFN. For example, WO2013163628 A2, Genetic Correction ofMutated Genes, published application of Duke University describesefforts to correct, for example, a frameshift mutation which causes apremature stop codon and a truncated gene product that can be correctedvia nuclease mediated non-homologous end joining such as thoseresponsible for Duchenne Muscular Dystrophy, (“DMD”) a recessive, fatal,X-linked disorder that results in muscle degeneration due to mutationsin the dystrophin gene. The majority of dystrophin mutations that causeDMD are deletions of exons that disrupt the reading frame and causepremature translation termination in the dystrophin gene. Dystrophin isa cytoplasmic protein that provides structural stability to thedystroglycan complex of the cell membrane that is responsible forregulating muscle cell integrity and function. The dystrophin gene or“DMD gene” as used interchangeably herein is 2.2 megabases at locusXp21. The primary transcription measures about 2,400 kb with the maturemRNA being about 14 kb. 79 exons code for the protein which is over 3500amino acids. Exon 51 is frequently adjacent to frame-disruptingdeletions in DMD patients and has been targeted in clinical trials foroligonucleotide-based exon skipping. A clinical trial for the exon 51skipping compound eteplirsen recently reported a significant functionalbenefit across 48 weeks, with an average of 47% dystrophin positivefibers compared to baseline. Mutations in exon 51 are ideally suited forpermanent correction by NHEJ-based genome editing.

The methods of US Patent Publication No. 20130145487 assigned toCellectis, which relates to meganuclease variants to cleave a targetsequence from the human dystrophin gene (DMD), may also be modified tofor the CRISPR Cas system of the present invention.

The invention uses nucleic acids to bind target DNA sequences. This isadvantageous as nucleic acids are much easier and cheaper to producethan proteins, and the specificity can be varied according to the lengthof the stretch where homology is sought. Complex 3-D positioning ofmultiple fingers, for example is not required.

The terms “polynucleotide”, “nucleotide”, “nucleotide sequence”,“nucleic acid” and “oligonucleotide” are used interchangeably. Theyrefer to a polymeric form of nucleotides of any length, eitherdeoxyribonucleotides or ribonucleotides, or analogs thereof.Polynucleotides may have any three dimensional structure, and mayperform any function, known or unknown. The following are non-limitingexamples of polynucleotides: coding or non-coding regions of a gene orgene fragment, loci (locus) defined from linkage analysis, exons,introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, shortinterfering RNA (siRNA), short-hairpin RNA (shRNA), micro-RNA (miRNA),ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides,plasmids, vectors, isolated DNA of any sequence, isolated RNA of anysequence, nucleic acid probes, and primers. The term also encompassesnucleic-acid-like structures with synthetic backbones, see, e.g.,Eckstein, 1991; Baserga et al., 1992; Milligan, 1993; WO 97/03211; WO96/39154; Mata, 1997; Strauss-Soukup, 1997; and Samstag, 1996. Apolynucleotide may comprise one or more modified nucleotides, such asmethylated nucleotides and nucleotide analogs. If present, modificationsto the nucleotide structure may be imparted before or after assembly ofthe polymer. The sequence of nucleotides may be interrupted bynon-nucleotide components. A polynucleotide may be further modifiedafter polymerization, such as by conjugation with a labeling component.

As used herein the term “wild type” is a term of the art understood byskilled persons and means the typical form of an organism, strain, geneor characteristic as it occurs in nature as distinguished from mutant orvariant forms.

As used herein the term “variant” should be taken to mean the exhibitionof qualities that have a pattern that deviates from what occurs innature.

The terms “non-naturally occurring” or “engineered” are usedinterchangeably and indicate the involvement of the hand of man. Theterms, when referring to nucleic acid molecules or polypeptides meanthat the nucleic acid molecule or the polypeptide is at leastsubstantially free from at least one other component with which they arenaturally associated in nature and as found in nature.

“Complementarity” refers to the ability of a nucleic acid to formhydrogen bond(s) with another nucleic acid sequence by eithertraditional Watson-Crick base pairing or other non-traditional types. Apercent complementarity indicates the percentage of residues in anucleic acid molecule which can form hydrogen bonds (e.g., Watson-Crickbase pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9,10 out of 10 being 50%, 60%, 70%, 80%, 90%, and 100% complementary).“Perfectly complementary” means that all the contiguous residues of anucleic acid sequence will hydrogen bond with the same number ofcontiguous residues in a second nucleic acid sequence. “Substantiallycomplementary” as used herein refers to a degree of complementarity thatis at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or100% over a region of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25, 30, 35, 40, 45, 50, or more nucleotides, or refersto two nucleic acids that hybridize under stringent conditions.

As used herein, “stringent conditions” for hybridization refer toconditions under which a nucleic acid having complementarity to a targetsequence predominantly hybridizes with the target sequence, andsubstantially does not hybridize to non-target sequences. Stringentconditions are generally sequence-dependent, and vary depending on anumber of factors. In general, the longer the sequence, the higher thetemperature at which the sequence specifically hybridizes to its targetsequence. Non-limiting examples of stringent conditions are described indetail in Tijssen (1993), Laboratory Techniques In Biochemistry AndMolecular Biology-Hybridization With Nucleic Acid Probes Part I, SecondChapter “Overview of principles of hybridization and the strategy ofnucleic acid probe assay”, Elsevier, N.Y. Where reference is made to apolynucleotide sequence, then complementary or partially complementarysequences are also envisaged. These are preferably capable ofhybridising to the reference sequence under highly stringent conditions.Generally, in order to maximize the hybridization rate, relativelylow-stringency hybridization conditions are selected: about 20 to 25° C.lower than the thermal melting point (T_(m)). The T_(m) is thetemperature at which 50% of specific target sequence hybridizes to aperfectly complementary probe in solution at a defined ionic strengthand pH. Generally, in order to require at least about 85% nucleotidecomplementarity of hybridized sequences, highly stringent washingconditions are selected to be about 5 to 15° C. lower than the T_(m). Inorder to require at least about 70% nucleotide complementarity ofhybridized sequences, moderately-stringent washing conditions areselected to be about 15 to 30° C. lower than the T_(m). Highlypermissive (very low stringency) washing conditions may be as low as 50°C. below the T_(m), allowing a high level of mis-matching betweenhybridized sequences. Those skilled in the art will recognize that otherphysical and chemical parameters in the hybridization and wash stagescan also be altered to affect the outcome of a detectable hybridizationsignal from a specific level of homology between target and probesequences. Preferred highly stringent conditions comprise incubation in50% formamide, 5×SSC, and 1% SDS at 42° C., or incubation in 5×SSC and1% SDS at 65° C., with wash in 0.2×SSC and 0.1% SDS at 65° C.

“Hybridization” refers to a reaction in which one or morepolynucleotides react to form a complex that is stabilized via hydrogenbonding between the bases of the nucleotide residues. The hydrogenbonding may occur by Watson Crick base pairing, Hoogstein binding, or inany other sequence specific manner. The complex may comprise two strandsforming a duplex structure, three or more strands forming a multistranded complex, a single self-hybridizing strand, or any combinationof these. A hybridization reaction may constitute a step in a moreextensive process, such as the initiation of PCR, or the cleavage of apolynucleotide by an enzyme. A sequence capable of hybridizing with agiven sequence is referred to as the “complement” of the given sequence.

As used herein, the term “genomic locus” or “locus” (plural loci) is thespecific location of a gene or DNA sequence on a chromosome. A “gene”refers to stretches of DNA or RNA that encode a polypeptide or an RNAchain that has functional role to play in an organism and hence is themolecular unit of heredity in living organisms. For the purpose of thisinvention it may be considered that genes include regions which regulatethe production of the gene product, whether or not such regulatorysequences are adjacent to coding and/or transcribed sequences.Accordingly, a gene includes, but is not necessarily limited to,promoter sequences, terminators, translational regulatory sequences suchas ribosome binding sites and internal ribosome entry sites, enhancers,silencers, insulators, boundary elements, replication origins, matrixattachment sites and locus control regions.

As used herein, “expression of a genomic locus” or “gene expression” isthe process by which information from a gene is used in the synthesis ofa functional gene product. The products of gene expression are oftenproteins, but in non-protein coding genes such as rRNA genes or tRNAgenes, the product is functional RNA. The process of gene expression isused by all known life—eukaryotes (including multicellular organisms),prokaryotes (bacteria and archaea) and viruses to generate functionalproducts to survive. As used herein “expression” of a gene or nucleicacid encompasses not only cellular gene expression, but also thetranscription and translation of nucleic acid(s) in cloning systems andin any other context. As used herein, “expression” also refers to theprocess by which a polynucleotide is transcribed from a DNA template(such as into and mRNA or other RNA transcript) and/or the process bywhich a transcribed mRNA is subsequently translated into peptides,polypeptides, or proteins. Transcripts and encoded polypeptides may becollectively referred to as “gene product.” If the polynucleotide isderived from genomic DNA, expression may include splicing of the mRNA ina eukaryotic cell.

The terms “polypeptide”, “peptide” and “protein” are usedinterchangeably herein to refer to polymers of amino acids of anylength. The polymer may be linear or branched, it may comprise modifiedamino acids, and it may be interrupted by non amino acids. The termsalso encompass an amino acid polymer that has been modified; forexample, disulfide bond formation, glycosylation, lipidation,acetylation, phosphorylation, or any other manipulation, such asconjugation with a labeling component. As used herein the term “aminoacid” includes natural and/or unnatural or synthetic amino acids,including glycine and both the D or L optical isomers, and amino acidanalogs and peptidomimetics.

As used herein, the term “domain” or “protein domain” refers to a partof a protein sequence that may exist and function independently of therest of the protein chain.

As described in aspects of the invention, sequence identity is relatedto sequence homology. Homology comparisons may be conducted by eye, ormore usually, with the aid of readily available sequence comparisonprograms. These commercially available computer programs may calculatepercent (%) homology between two or more sequences and may alsocalculate the sequence identity shared by two or more amino acid ornucleic acid sequences. In some preferred embodiments, the cappingregion of the dTALEs described herein have sequences that are at least95% identical or share identity to the capping region amino acidsequences provided herein.

Sequence homologies may be generated by any of a number of computerprograms known in the art, for example BLAST or FASTA, etc. A suitablecomputer program for carrying out such an alignment is the GCG WisconsinBestfit package (University of Wisconsin, U.S.A; Devereux et al., 1984,Nucleic Acids Research 12:387). Examples of other software than mayperform sequence comparisons include, but are not limited to, the BLASTpackage (see Ausubel et al., 1999 ibid—Chapter 18), FASTA (Atschul etal., 1990, J. Mol. Biol., 403-410) and the GENEWORKS suite of comparisontools. Both BLAST and FASTA are available for offline and onlinesearching (see Ausubel et al., 1999 ibid, pages 7-58 to 7-60). Howeverit is preferred to use the GCG Bestfit program.

Percentage (%) sequence homology may be calculated over contiguoussequences, i.e., one sequence is aligned with the other sequence andeach amino acid or nucleotide in one sequence is directly compared withthe corresponding amino acid or nucleotide in the other sequence, oneresidue at a time. This is called an “ungapped” alignment. Typically,such ungapped alignments are performed only over a relatively shortnumber of residues.

Although this is a very simple and consistent method, it fails to takeinto consideration that, for example, in an otherwise identical pair ofsequences, one insertion or deletion may cause the following amino acidresidues to be put out of alignment, thus potentially resulting in alarge reduction in % homology when a global alignment is performed.Consequently, most sequence comparison methods are designed to produceoptimal alignments that take into consideration possible insertions anddeletions without unduly penalizing the overall homology or identityscore. This is achieved by inserting “gaps” in the sequence alignment totry to maximize local homology or identity.

However, these more complex methods assign “gap penalties” to each gapthat occurs in the alignment so that, for the same number of identicalamino acids, a sequence alignment with as few gaps aspossible—reflecting higher relatedness between the two comparedsequences—may achieve a higher score than one with many gaps. “Affinitygap costs” are typically used that charge a relatively high cost for theexistence of a gap and a smaller penalty for each subsequent residue inthe gap. This is the most commonly used gap scoring system. High gappenalties may, of course, produce optimized alignments with fewer gaps.Most alignment programs allow the gap penalties to be modified. However,it is preferred to use the default values when using such software forsequence comparisons. For example, when using the GCG Wisconsin Bestfitpackage the default gap penalty for amino acid sequences is −12 for agap and −4 for each extension.

Calculation of maximum % homology therefore first requires theproduction of an optimal alignment, taking into consideration gappenalties. A suitable computer program for carrying out such analignment is the GCG Wisconsin Bestfit package (Devereux et al., 1984Nuc. Acids Research 12 p 387). Examples of other software that mayperform sequence comparisons include, but are not limited to, the BLASTpackage (see Ausubel et al., 1999 Short Protocols in Molecular Biology,4 h Ed.—Chapter 18), FASTA (Altschul et al., 1990 J. Mol. Biol. 403-410)and the GENEWORKS suite of comparison tools. Both BLAST and FASTA areavailable for offline and online searching (see Ausubel et al., 1999,Short Protocols in Molecular Biology, pages 7-58 to 7-60). However, forsome applications, it is preferred to use the GCG Bestfit program. A newtool, called BLAST 2 Sequences is also available for comparing proteinand nucleotide sequences (see FEMS Microbiol Lett. 1999 174(2): 247-50;FEAMS Microbiol Lett. 1999 177(1): 187-8 and the website of the NationalCenter for Biotechnology information at the website of the NationalInstitutes for Health).

Although the final % homology may be measured in terms of identity, thealignment process itself is typically not based on an all-or-nothingpair comparison. Instead, a scaled similarity score matrix is generallyused that assigns scores to each pair-wise comparison based on chemicalsimilarity or evolutionary distance. An example of such a matrixcommonly used is the BLOSUM62 matrix—the default matrix for the BLASTsuite of programs. GCG Wisconsin programs generally use either thepublic default values or a custom symbol comparison table, if supplied(see user manual for further details). For some applications, it ispreferred to use the public default values for the GCG package, or inthe case of other software, the default matrix, such as BLOSUM62.

Alternatively, percentage homologies may be calculated using themultiple alignment feature in DNASIS™ (Hitachi Software), based on analgorithm, analogous to CLUSTAL (Higgins D G & Sharp P M (1988), Gene73(1), 237-244). Once the software has produced an optimal alignment, itis possible to calculate % homology, preferably % sequence identity. Thesoftware typically does this as part of the sequence comparison andgenerates a numerical result.

The sequences may also have deletions, insertions or substitutions ofamino acid residues which produce a silent change and result in afunctionally equivalent substance. Deliberate amino acid substitutionsmay be made on the basis of similarity in amino acid properties (such aspolarity, charge, solubility, hydrophobicity, hydrophilicity, and/or theamphipathic nature of the residues) and it is therefore useful to groupamino acids together in functional groups. Amino acids may be groupedtogether based on the properties of their side chains alone. However, itis more useful to include mutation data as well. The sets of amino acidsthus derived are likely to be conserved for structural reasons. Thesesets may be described in the form of a Venn diagram (Livingstone C. D.and Barton G. J. (1993) “Protein sequence alignments: a strategy for thehierarchical analysis of residue conservation” Comput. Appl. Biosci. 9:745-756) (Taylor W. R. (1986) “The classification of amino acidconservation” J. Theor. Biol. 119; 205-218). Conservative substitutionsmay be made, for example according to the table below which describes agenerally accepted Venn diagram grouping of amino acids.

Set SuB-set Hydrophobic F M I L V A G C Aromatic F W Y H Aliphatic I L VPolar W Y H K R E D C S T N Q Charged H K R E D Positively H K R chargedNegatively E D charged Small V C A G S P T N D Tiny A G S

Embodiments of the invention include sequences (both polynucleotide orpolypeptide) which may comprise homologous substitution (substitutionand replacement are both used herein to mean the interchange of anexisting amino acid residue or nucleotide, with an alternative residueor nucleotide) that may occur i.e., like-for-like substitution in thecase of amino acids such as basic for basic, acidic for acidic, polarfor polar, etc. Non-homologous substitution may also occur i.e., fromone class of residue to another or alternatively involving the inclusionof unnatural amino acids such as ornithine (hereinafter referred to asZ), diaminobutyric acid ornithine (hereinafter referred to as B),norleucine ornithine (hereinafter referred to as O), pyriylalanine,thienylalanine, naphthylalanine and phenylglycine.

Variant amino acid sequences may include suitable spacer groups that maybe inserted between any two amino acid residues of the sequenceincluding alkyl groups such as methyl, ethyl or propyl groups inaddition to amino acid spacers such as glycine or β-alanine residues. Afurther form of variation, which involves the presence of one or moreamino acid residues in peptoid form, may be well understood by thoseskilled in the art. For the avoidance of doubt, “the peptoid form” isused to refer to variant amino acid residues wherein the α-carbonsubstituent group is on the residue's nitrogen atom rather than theα-carbon. Processes for preparing peptides in the peptoid form are knownin the art, for example Simon R J et al., PNAS (1992) 89(20), 9367-9371and Horwell D C, Trends Biotechnol. (1995) 13(4), 132-134.

The practice of the present invention employs, unless otherwiseindicated, conventional techniques of immunology, biochemistry,chemistry, molecular biology, microbiology, cell biology, genomics andrecombinant DNA, which are within the skill of the art. See Sambrook,Fritsch and Maniatis, MOLECULAR CLONING: A LABORATORY MANUAL, 2ndedition (1989); CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (F. M. Ausubel,et al. eds., (1987)); the series METHODS IN ENZYMOLOGY (Academic Press,Inc.): PCR 2: A PRACTICAL APPROACH (M. J. MacPherson, B. D. Hames and G.R. Taylor eds. (1995)), Harlow and Lane, eds. (1988) ANTIBODIES, ALABORATORY MANUAL, and ANIMAL CELL CULTURE (R.I. Freshney, ed. (1987)).

In one aspect, the invention provides for vectors that are used in theengineering and optimization of CRISPR-Cas systems.

A used herein, a “vector” is a tool that allows or facilitates thetransfer of an entity from one environment to another. It is a replicon,such as a plasmid, phage, or cosmid, into which another DNA segment maybe inserted so as to bring about the replication of the insertedsegment. Generally, a vector is capable of replication when associatedwith the proper control elements. In general, the term “vector” refersto a nucleic acid molecule capable of transporting another nucleic acidto which it has been linked. Vectors include, but are not limited to,nucleic acid molecules that are single-stranded, double-stranded, orpartially double-stranded; nucleic acid molecules that comprise one ormore free ends, no free ends (e.g. circular); nucleic acid moleculesthat comprise DNA, RNA, or both; and other varieties of polynucleotidesknown in the art. One type of vector is a “plasmid,” which refers to acircular double stranded DNA loop into which additional DNA segments canbe inserted, such as by standard molecular cloning techniques. Anothertype of vector is a viral vector, wherein virally-derived DNA or RNAsequences are present in the vector for packaging into a virus (e.g.retroviruses, replication defective retroviruses, adenoviruses,replication defective adenoviruses, and adeno-associated viruses(AAVs)). Viral vectors also include polynucleotides carried by a virusfor transfection into a host cell. Certain vectors are capable ofautonomous replication in a host cell into which they are introduced(e.g. bacterial vectors having a bacterial origin of replication andepisomal mammalian vectors). Other vectors (e.g., non-episomal mammalianvectors) are integrated into the genome of a host cell upon introductioninto the host cell, and thereby are replicated along with the hostgenome. Moreover, certain vectors are capable of directing theexpression of genes to which they are operatively-linked. Such vectorsare referred to herein as “expression vectors.” Common expressionvectors of utility in recombinant DNA techniques are often in the formof plasmids.

Recombinant expression vectors can comprise a nucleic acid of theinvention in a form suitable for expression of the nucleic acid in ahost cell, which means that the recombinant expression vectors includeone or more regulatory elements, which may be selected on the basis ofthe host cells to be used for expression, that is operatively-linked tothe nucleic acid sequence to be expressed. Within a recombinantexpression vector, “operably linked” is intended to mean that thenucleotide sequence of interest is linked to the regulatory element(s)in a manner that allows for expression of the nucleotide sequence (e.g.in an in vitro transcription/translation system or in a host cell whenthe vector is introduced into the host cell). With regards torecombination and cloning methods, mention is made of U.S. patentapplication Ser. No. 10/815,730, published Sep. 2, 2004 as US2004-0171156 A1, the contents of which are herein incorporated byreference in their entirety.

Aspects of the invention relate to bicistronic vectors for chimeric RNAand Cas9. Bicistronic expression vectors for chimeric RNA and Cas9 arepreferred. In general and particularly in this embodiment Cas9 ispreferably driven by the CBh promoter. The chimeric RNA may preferablybe driven by a U6 promoter. Ideally the two are combined. The chimericguide RNA typically consists of a 20 bp guide sequence (Ns) and this maybe joined to the tracr sequence (running from the first “U” of the lowerstrand to the end of the transcript). The tracr sequence may betruncated at various positions as indicated. The guide and tracrsequences are separated by the tracr-mate sequence, which may beGUUUUAGAGCUA. This may be followed by the loop sequence GAAA as shown.Both of these are preferred examples. Applicants have demonstratedCas9-mediated indels at the human EMX1 and PVALB loci by SURVEYORassays. ChiRNAs are indicated by their “+n” designation, and crRNArefers to a hybrid RNA where guide and tracr sequences are expressed asseparate transcripts. Throughout this application, chimeric RNA may alsobe called single guide, or synthetic guide RNA (sgRNA). The loop ispreferably GAAA, but it is not limited to this sequence or indeed tobeing only 4 bp in length. Indeed, preferred loop forming sequences foruse in hairpin structures are four nucleotides in length, and mostpreferably have the sequence GAAA. However, longer or shorter loopsequences may be used, as may alternative sequences. The sequencespreferably include a nucleotide triplet (for example, AAA), and anadditional nucleotide (for example C or G). Examples of loop formingsequences include CAAA and AAAG.

The term “regulatory element” is intended to include promoters,enhancers, internal ribosomal entry sites (IRES), and other expressioncontrol elements (e.g. transcription termination signals, such aspolyadenylation signals and poly-U sequences). Such regulatory elementsare described, for example, in Goeddel, GENE EXPRESSION TECHNOLOGY:METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990).Regulatory elements include those that direct constitutive expression ofa nucleotide sequence in many types of host cell and those that directexpression of the nucleotide sequence only in certain host cells (e.g.,tissue-specific regulatory sequences). A tissue-specific promoter maydirect expression primarily in a desired tissue of interest, such asmuscle, neuron, bone, skin, blood, specific organs (e.g. liver,pancreas), or particular cell types (e.g. lymphocytes). Regulatoryelements may also direct expression in a temporal-dependent manner, suchas in a cell-cycle dependent or developmental stage-dependent manner,which may or may not also be tissue or cell-type specific. In someembodiments, a vector comprises one or more pol III promoter (e.g. 1, 2,3, 4, 5, or more pol III promoters), one or more pol II promoters (e.g.1, 2, 3, 4, 5, or more pol II promoters), one or more pol I promoters(e.g. 1, 2, 3, 4, 5, or more pol I promoters), or combinations thereof.Examples of pol III promoters include, but are not limited to, U6 and H1promoters. Examples of pol II promoters include, but are not limited to,the retroviral Rous sarcoma virus (RSV) LTR promoter (optionally withthe RSV enhancer), the cytomegalovirus (CMV) promoter (optionally withthe CMV enhancer) [see, e.g., Boshart et al, Cell, 41:521-530 (1985)],the SV40 promoter, the dihydrofolate reductase promoter, the β-actinpromoter, the phosphoglycerol kinase (PGK) promoter, and the EF1αpromoter. Also encompassed by the term “regulatory element” are enhancerelements, such as WPRE; CMV enhancers; the R-U5′ segment in LTR ofHTLV-I (Mol. Cell. Biol., Vol. 8(1), p. 466-472, 1988); SV40 enhancer;and the intron sequence between exons 2 and 3 of rabbit β-globin (Proc.Natl. Acad. Sci. USA., Vol. 78(3), p. 1527-31, 1981). It will beappreciated by those skilled in the art that the design of theexpression vector can depend on such factors as the choice of the hostcell to be transformed, the level of expression desired, etc. A vectorcan be introduced into host cells to thereby produce transcripts,proteins, or peptides, including fusion proteins or peptides, encoded bynucleic acids as described herein (e.g., clustered regularlyinterspersed short palindromic repeats (CRISPR) transcripts, proteins,enzymes, mutant forms thereof, fusion proteins thereof, etc.). Withregards to regulatory sequences, mention is made of U.S. patentapplication Ser. No. 10/491,026, the contents of which are incorporatedby reference herein in their entirety. With regards to promoters,mention is made of PCT publication WO 2011/028929 and U.S. applicationSer. No. 12/511,940, the contents of which are incorporated by referenceherein in their entirety.

Vectors can be designed for expression of CRISPR transcripts (e.g.nucleic acid transcripts, proteins, or enzymes) in prokaryotic oreukaryotic cells. For example, CRISPR transcripts can be expressed inbacterial cells such as Escherichia coli, insect cells (usingbaculovirus expression vectors), yeast cells, or mammalian cells.Suitable host cells are discussed further in Goeddel, GENE EXPRESSIONTECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif.(1990). Alternatively, the recombinant expression vector can betranscribed and translated in vitro, for example using T7 promoterregulatory sequences and T7 polymerase.

Vectors may be introduced and propagated in a prokaryote or prokaryoticcell. In some embodiments, a prokaryote is used to amplify copies of avector to be introduced into a eukaryotic cell or as an intermediatevector in the production of a vector to be introduced into a eukaryoticcell (e.g. amplifying a plasmid as part of a viral vector packagingsystem). In some embodiments, a prokaryote is used to amplify copies ofa vector and express one or more nucleic acids, such as to provide asource of one or more proteins for delivery to a host cell or hostorganism. Expression of proteins in prokaryotes is most often carriedout in Escherichia coli with vectors containing constitutive orinducible promoters directing the expression of either fusion ornon-fusion proteins. Fusion vectors add a number of amino acids to aprotein encoded therein, such as to the amino terminus of therecombinant protein. Such fusion vectors may serve one or more purposes,such as: (i) to increase expression of recombinant protein; (ii) toincrease the solubility of the recombinant protein; and (iii) to aid inthe purification of the recombinant protein by acting as a ligand inaffinity purification. Often, in fusion expression vectors, aproteolytic cleavage site is introduced at the junction of the fusionmoiety and the recombinant protein to enable separation of therecombinant protein from the fusion moiety subsequent to purification ofthe fusion protein. Such enzymes, and their cognate recognitionsequences, include Factor Xa, thrombin and enterokinase. Example fusionexpression vectors include pGEX (Pharmacia Biotech Inc; Smith andJohnson, 1988. Gene 67: 31-40), pMAL (New England Biolabs, Beverly,Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.) that fuse glutathioneS-transferase (GST), maltose E binding protein, or protein A,respectively, to the target recombinant protein.

Examples of suitable inducible non-fusion E. coli expression vectorsinclude pTrc (Amrann et al., (1988) Gene 69:301-315) and pET 11d(Studier et al., GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185,Academic Press, San Diego, Calif. (1990) 60-89).

In some embodiments, a vector is a yeast expression vector. Examples ofvectors for expression in yeast Saccharomyces cerivisae include pYepSec1(Baldari, et al., 1987. EMBO J. 6: 229-234), pMFa (Kuijan andHerskowitz, 1982. Cell 30: 933-943), pJRY88 (Schultz et al., 1987. Gene54: 113-123), pYES2 (Invitrogen Corporation, San Diego, Calif.), andpicZ (InVitrogen Corp, San Diego, Calif.).

In some embodiments, a vector drives protein expression in insect cellsusing baculovirus expression vectors. Baculovirus vectors available forexpression of proteins in cultured insect cells (e.g., SF9 cells)include the pAc series (Smith, et al., 1983. Mol. Cell. Biol. 3:2156-2165) and the pVL series (Lucklow and Summers, 1989. Virology 170:31-39).

In some embodiments, a vector is capable of driving expression of one ormore sequences in mammalian cells using a mammalian expression vector.Examples of mammalian expression vectors include pCDM8 (Seed, 1987.Nature 329: 840) and pMT2PC (Kaufman, et al., 1987. EMBO J. 6: 187-195).When used in mammalian cells, the expression vector's control functionsare typically provided by one or more regulatory elements. For example,commonly used promoters are derived from polyoma, adenovirus 2,cytomegalovirus, simian virus 40, and others disclosed herein and knownin the art. For other suitable expression systems for both prokaryoticand eukaryotic cells see, e.g., Chapters 16 and 17 of Sambrook, et al.,MOLECULAR CLONING: A LABORATORY MANUAL. 2nd ed., Cold Spring HarborLaboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor,N.Y., 1989.

In some embodiments, the recombinant mammalian expression vector iscapable of directing expression of the nucleic acid preferentially in aparticular cell type (e.g., tissue-specific regulatory elements are usedto express the nucleic acid). Tissue-specific regulatory elements areknown in the art. Non-limiting examples of suitable tissue-specificpromoters include the albumin promoter (liver-specific; Pinkert, et al.,1987. Genes Dev. 1: 268-277), lymphoid-specific promoters (Calame andEaton, 1988. Adv. Immunol. 43: 235-275), in particular promoters of Tcell receptors (Winoto and Baltimore, 1989. EMBO J. 8: 729-733) andimmunoglobulins (Baneiji, et al., 1983. Cell 33: 729-740; Queen andBaltimore, 1983. Cell 33: 741-748), neuron-specific promoters (e.g., theneurofilament promoter; Byrne and Ruddle, 1989. Proc. Natl. Acad. Sci.USA 86: 5473-5477), pancreas-specific promoters (Edlund, et al., 1985.Science 230: 912-916), and mammary gland-specific promoters (e.g., milkwhey promoter; U.S. Pat. No. 4,873,316 and European ApplicationPublication No. 264, 166). Developmentally-regulated promoters are alsoencompassed, e.g., the murine hox promoters (Kessel and Gruss, 1990.Science 249: 374-379) and the α-fetoprotein promoter (Campes andTilghman, 1989. Genes Dev. 3: 537-546). With regards to theseprokaryotic and eukaryotic vectors, mention is made of U.S. Pat. No.6,750,059, the contents of which are incorporated by reference herein intheir entirety. Other embodiments of the invention may relate to the useof viral vectors, with regards to which mention is made of U.S. patentapplication Ser. No. 13/092,085, the contents of which are incorporatedby reference herein in their entirety. Tissue-specific regulatoryelements are known in the art and in this regard, mention is made ofU.S. Pat. No. 7,776,321, the contents of which are incorporated byreference herein in their entirety.

In some embodiments, a regulatory element is operably linked to one ormore elements of a CRISPR system so as to drive expression of the one ormore elements of the CRISPR system. In general, CRISPRs (ClusteredRegularly Interspaced Short Palindromic Repeats), also known as SPIDRs(SPacer Interspersed Direct Repeats), constitute a family of DNA locithat are usually specific to a particular bacterial species. The CRISPRlocus comprises a distinct class of interspersed short sequence repeats(SSRs) that were recognized in E. coli (Ishino et al., J. Bacteriol.,169:5429-5433 [1987]; and Nakata et al., J. Bacteriol., 171:3553-3556[1989]), and associated genes. Similar interspersed SSRs have beenidentified in Haloferax mediterranei, Streptococcus pyogenes, Anabaena,and Mycobacterium tuberculosis (See, Groenen et al., Mol. Microbiol.,10:1057-1065 [1993]; Hoe et al., Emerg. Infect. Dis., 5:254-263 [1999];Masepohl et al., Biochim. Biophys. Acta 1307:26-30 [1996]; and Mojica etal., Mol. Microbiol., 17:85-93 [1995]). The CRISPR loci typically differfrom other SSRs by the structure of the repeats, which have been termedshort regularly spaced repeats (SRSRs) (Janssen et al., OMICS J. Integ.Biol., 6:23-33 [2002]; and Mojica et al., Mol. Microbiol., 36:244-246[2000]). In general, the repeats are short elements that occur inclusters that are regularly spaced by unique intervening sequences witha substantially constant length (Mojica et al., [2000], supra). Althoughthe repeat sequences are highly conserved between strains, the number ofinterspersed repeats and the sequences of the spacer regions typicallydiffer from strain to strain (van Embden et al., J. Bacteriol.,182:2393-2401 [2000]). CRISPR loci have been identified in more than 40prokaryotes (See e.g., Jansen et al., Mol. Microbiol., 43:1565-1575[2002]; and Mojica et al., [2005]) including, but not limited toAeropyrum, Pyrobaculum, Sulfolobus, Archaeoglobus, Halocarcula,Methanobacterium, Methanococcus, Methanosarcina, Methanopyrus,Pyrococcus, Picrophilus, Thermoplasma, Corynebacterium, Mycobacterium,Streptomyces, Aquifex, Porphyromonas, Chlorobium, Thermus, Bacillus,Listeria, Staphylococcus, Clostridium, Thermoanaerobacter, Mycoplasma,Fusobacterium, Azarcus, Chromobacterium, Neisseria, Nitrosomonas,Desulfovibrio, Geobacter, Myxococcus, Canmpylobacter, Wolinella,Acinetobacter, Erwinia, Escherichia, Legionella, Methylococcus,Pasteurella, Photobacterium, Salmonella, Xanthomonas, Yersinia,Treponema, and Thermotoga.

In general, “CRISPR system” refers collectively to transcripts and otherelements involved in the expression of or directing the activity ofCRISPR-associated (“Cas”) genes, including sequences encoding a Casgene, a tracr (trans-activating CRISPR) sequence (e.g. tracrRNA or anactive partial tracrRNA), a tracr-mate sequence (encompassing a “directrepeat” and a tracrRNA-processed partial direct repeat in the context ofan endogenous CRISPR system), a guide sequence (also referred to as a“spacer” in the context of an endogenous CRISPR system), or othersequences and transcripts from a CRISPR locus. In embodiments of theinvention the terms guide sequence and guide RNA are usedinterchangeably. In some embodiments, one or more elements of a CRISPRsystem is derived from a type I, type II, or type III CRISPR system. Insome embodiments, one or more elements of a CRISPR system is derivedfrom a particular organism comprising an endogenous CRISPR system, suchas Streptococcus pyogenes. In general, a CRISPR system is characterizedby elements that promote the formation of a CRISPR complex at the siteof a target sequence (also referred to as a protospacer in the contextof an endogenous CRISPR system). In the context of formation of a CRISPRcomplex, “target sequence” refers to a sequence to which a guidesequence is designed to have complementarity, where hybridizationbetween a target sequence and a guide sequence promotes the formation ofa CRISPR complex. A target sequence may comprise any polynucleotide,such as DNA or RNA polynucleotides. In some embodiments, a targetsequence is located in the nucleus or cytoplasm of a cell.

In some embodiments, direct repeats may be identified in silico bysearching for repetitive motifs that fulfill any or all of the followingcriteria:

1. found in a 2 Kb window of genomic sequence flanking the type IICRISPR locus;

2. span from 20 to 50 bp; and

3. interspaced by 20 to 50 bp.

In some embodiments, 2 of these criteria may be used, for instance 1 and2, 2 and 3, or 1 and 3. In some embodiments, all 3 criteria may be used.

In some embodiments, candidate tracrRNA may be subsequently predicted bysequences that fulfill any or all of the following criteria:

1. sequence homology to direct repeats (motif search in Geneious with upto 18-bp mismatches);

2. presence of a predicted Rho-independent transcriptional terminator indirection of transcription; and

3. stable hairpin secondary structure between tracrRNA and directrepeat.

In some embodiments, 2 of these criteria may be used, for instance 1 and2, 2 and 3, or 1 and 3. In some embodiments, all 3 criteria may be used.

In some embodiments, chimeric synthetic guide RNAs (sgRNAs) designs mayincorporate at least 12 bp of duplex structure between the direct repeatand tracrRNA.

In preferred embodiments of the invention, the CRISPR system is a typeII CRISPR system and the Cas enzyme is Cas9, which catalyzes DNAcleavage. Enzymatic action by Cas9 derived from Streptococcus pyogenesor any closely related Cas9 generates double stranded breaks at targetsite sequences which hybridize to 20 nucleotides of the guide sequenceand that have a protospacer-adjacent motif (PAM) sequence (examplesinclude NGG/NRG or a PAM that can be determined as described herein)following the 20 nucleotides of the target sequence. CRISPR activitythrough Cas9 for site-specific DNA recognition and cleavage is definedby the guide sequence, the tracr sequence that hybridizes in part to theguide sequence and the PAM sequence. More aspects of the CRISPR systemare described in Karginov and Hannon, The CRISPR system: smallRNA-guided defense in bacteria and archaea, Mole Cell 2010, Jan. 15;37(1): 7.

The type II CRISPR locus from Streptococcus pyogenes SF370 contains acluster of four genes Cas9, Cas1, Cas2, and Csn1, as well as twonon-coding RNA elements, tracrRNA and a characteristic array ofrepetitive sequences (direct repeats) interspaced by short stretches ofnon-repetitive sequences (spacers, about 30 bp each). In this system,targeted DNA double-strand break (DSB) is generated in four sequentialsteps (FIG. 2A). First, two non-coding RNAs, the pre-crRNA array andtracrRNA, are transcribed from the CRISPR locus. Second, tracrRNAhybridizes to the direct repeats of pre-crRNA, which is then processedinto mature crRNAs containing individual spacer sequences. Third, themature crRNA:tracrRNA complex directs Cas9 to the DNA target consistingof the protospacer and the corresponding PAM via heteroduplex formationbetween the spacer region of the crRNA and the protospacer DNA. Finally,Cas9 mediates cleavage of target DNA upstream of PAM to create a DSBwithin the protospacer (FIG. 2A). FIG. 2B demonstrates the nuclearlocalization of the codon optimized Cas9. To promote precisetranscriptional initiation, the RNA polymerase III-based U6 promoter wasselected to drive the expression of tracrRNA (FIG. 2C). Similarly, a U6promoter-based construct was developed to express a pre-crRNA arrayconsisting of a single spacer flanked by two direct repeats (DRs, alsoencompassed by the term “tracr-mate sequences”; FIG. 2C). The initialspacer was designed to target a 33-base-pair (bp) target site (30-bpprotospacer plus a 3-bp CRISPR motif (PAM) sequence satisfying the NGGrecognition motif of Cas9) in the human EMX1 locus (FIG. 2C), a key genein the development of the cerebral cortex.

Typically, in the context of an endogenous CRISPR system, formation of aCRISPR complex (comprising a guide sequence hybridized to a targetsequence and complexed with one or more Cas proteins) results incleavage of one or both strands in or near (e.g. within 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 20, 50, or more base pairs from) the target sequence.Without wishing to be bound by theory, the tracr sequence, which maycomprise or consist of all or a portion of a wild-type tracr sequence(e.g. about or more than about 20, 26, 32, 45, 48, 54, 63, 67, 85, ormore nucleotides of a wild-type tracr sequence), may also form part of aCRISPR complex, such as by hybridization along at least a portion of thetracr sequence to all or a portion of a tracr mate sequence that isoperably linked to the guide sequence. In some embodiments, one or morevectors driving expression of one or more elements of a CRISPR systemare introduced into a host cell such that expression of the elements ofthe CRISPR system direct formation of a CRISPR complex at one or moretarget sites. For example, a Cas enzyme, a guide sequence linked to atracr-mate sequence, and a tracr sequence could each be operably linkedto separate regulatory elements on separate vectors. Alternatively, twoor more of the elements expressed from the same or different regulatoryelements, may be combined in a single vector, with one or moreadditional vectors providing any components of the CRISPR system notincluded in the first vector. CRISPR system elements that are combinedin a single vector may be arranged in any suitable orientation, such asone element located 5′ with respect to (“upstream” of) or 3′ withrespect to (“downstream” of) a second element. The coding sequence ofone element may be located on the same or opposite strand of the codingsequence of a second element, and oriented in the same or oppositedirection. In some embodiments, a single promoter drives expression of atranscript encoding a CRISPR enzyme and one or more of the guidesequence, tracr mate sequence (optionally operably linked to the guidesequence), and a tracr sequence embedded within one or more intronsequences (e.g. each in a different intron, two or more in at least oneintron, or all in a single intron). In some embodiments, the CRISPRenzyme, guide sequence, tracr mate sequence, and tracr sequence areoperably linked to and expressed from the same promoter.

In some embodiments, a vector comprises one or more insertion sites,such as a restriction endonuclease recognition sequence (also referredto as a “cloning site”). In some embodiments, one or more insertionsites (e.g. about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ormore insertion sites) are located upstream and/or downstream of one ormore sequence elements of one or more vectors. In some embodiments, avector comprises an insertion site upstream of a tracr mate sequence,and optionally downstream of a regulatory element operably linked to thetracr mate sequence, such that following insertion of a guide sequenceinto the insertion site and upon expression the guide sequence directssequence-specific binding of a CRISPR complex to a target sequence in aeukaryotic cell. In some embodiments, a vector comprises two or moreinsertion sites, each insertion site being located between two tracrmate sequences so as to allow insertion of a guide sequence at eachsite. In such an arrangement, the two or more guide sequences maycomprise two or more copies of a single guide sequence, two or moredifferent guide sequences, or combinations of these. When multipledifferent guide sequences are used, a single expression construct may beused to target CRISPR activity to multiple different, correspondingtarget sequences within a cell. For example, a single vector maycomprise about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20,or more guide sequences. In some embodiments, about or more than about1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more such guide-sequence-containingvectors may be provided, and optionally delivered to a cell.

In some embodiments, a vector comprises a regulatory element operablylinked to an enzyme-coding sequence encoding a CRISPR enzyme, such as aCas protein. Non-limiting examples of Cas proteins include Cas1, Cas 1B,Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csn1 andCsx12), Cas10, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2, Csa5, Csn2,Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2,Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2,Csf3, Csf4, homologues thereof, or modified versions thereof. In someembodiments, the unmodified CRISPR enzyme has DNA cleavage activity,such as Cas9. In some embodiments, the CRISPR enzyme directs cleavage ofone or both strands at the location of a target sequence, such as withinthe target sequence and/or within the complement of the target sequence.In some embodiments, the CRISPR enzyme directs cleavage of one or bothstrands within about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 50, 100,200, 500, or more base pairs from the first or last nucleotide of atarget sequence. In some embodiments, a vector encodes a CRISPR enzymethat is mutated to with respect to a corresponding wild-type enzyme suchthat the mutated CRISPR enzyme lacks the ability to cleave one or bothstrands of a target polynucleotide containing a target sequence. Forexample, an aspartate-to-alanine substitution (D10A) in the RuvC Icatalytic domain of Cas9 from S. pyogenes converts Cas9 from a nucleasethat cleaves both strands to a nickase (cleaves a single strand). Otherexamples of mutations that render Cas9 a nickase include, withoutlimitation, H840A, N854A, and N863A. As a further example, two or morecatalytic domains of Cas9 (RuvC I, RuvC II, and RuvC III or the HNHdomain) may be mutated to produce a mutated Cas9 substantially lackingall DNA cleavage activity. In some embodiments, a D10A mutation iscombined with one or more of H840A, N854A, or N863A mutations to producea Cas9 enzyme substantially lacking all DNA cleavage activity. In someembodiments, a CRISPR enzyme is considered to substantially lack all DNAcleavage activity when the DNA cleavage activity of the mutated enzymeis less than about 25%, 10%, 5%, 1%, 0.1%, 0.01%, or lower with respectto its non-mutated form. Where the enzyme is not SpCas9, mutations maybe made at any or all residues corresponding to positions 10, 762, 840,854, 863 and/or 986 of SpCas9 (which may be ascertained for instance bystandard sequence comparison tools). In particular, any or all of thefollowing mutations are preferred in SpCas9: D10A, E762A, H840A, N854A,N863A and/or D986A; as well as conservative substitution for any of thereplacement amino acids is also envisaged. The same (or conservativesubstitutions of these mutations) at corresponding positions in otherCas9s are also preferred. Particularly preferred are D10 and H840 inSpCas9. However, in other Cas9s, residues corresponding to SpCas9 D10and H840 are also preferred.

An aspartate-to-alanine substitution (D10A) in the RuvC I catalyticdomain of SpCas9 was engineered to convert the nuclease into a nickase(SpCas9n) (see e.g. Sapranauskas et al., 2011, Nucleic Acis Research,39: 9275; Gasiunas et al., 2012. Proc. Natl. Acad. Sci. USA, 109:E2579),such that nicked genomic DNA undergoes the high-fidelityhomology-directed repair (HDR). Surveyor assay confirmed that SpCas9ndoes not generate indels at the EMX1 protospacer target. Co-expressionof EMX1-targeting chimeric crRNA (having the tracrRNA component as well)with SpCas9 produced indels in the target site, whereas co-expressionwith SpCas9n did not (n=3). Moreover, sequencing of 327 amplicons didnot detect any indels induced by SpCas9n. The same locus was selected totest CRISPR-mediated HR by co-transfecting HEK 293FT cells with thechimeric RNA targeting EMX1, hSpCas9 or hSpCas9n, as well as a HRtemplate to introduce a pair of restriction sites (HindIII and NheI)near the protospacer.

Preferred orthologs are described herein. A Cas enzyme may be identifiedas Cas9 as this can refer to the general class of enzymes that sharehomology to the biggest nuclease with multiple nuclease domains from thetype II CRISPR system. Most preferably, the Cas9 enzyme is from, or isderived from, spCas9 or saCas9. By derived, Applicants mean that thederived enzyme is largely based, in the sense of having a high degree ofsequence homology with, a wildtype enzyme, but that it has been mutated(modified) in some way as described herein.

It will be appreciated that the terms Cas and CRISPR enzyme aregenerally used herein interchangeably, unless otherwise apparent. Asmentioned above, many of the residue numberings used herein refer to theCas9 enzyme from the type II CRISPR locus in Streptococcus pyogenes.However, it will be appreciated that this invention includes many moreCas9s from other species of microbes, such as SpCas9, SaCa9, St1Cas9 andso forth.

An example of a codon optimized sequence, in this instance optimized forhumans (i.e. being optimized for expression in humans) is providedherein, see the SaCas9 human codon optimized sequence. Whilst this ispreferred, it will be appreciated that other examples are possible andcodon optimization for a host species is known.

In some embodiments, an enzyme coding sequence encoding a CRISPR enzymeis codon optimized for expression in particular cells, such aseukaryotic cells. The eukaryotic cells may be those of or derived from aparticular organism, such as a mammal, including but not limited tohuman, mouse, rat, rabbit, dog, or non-human mammal or primate. In someembodiments, processes for modifying the germ line genetic identity ofhuman beings and/or processes for modifying the genetic identity ofanimals which are likely to cause them suffering without any substantialmedical benefit to man or animal, and also animals resulting from suchprocesses, may be excluded.

In general, codon optimization refers to a process of modifying anucleic acid sequence for enhanced expression in the host cells ofinterest by replacing at least one codon (e.g. about or more than about1, 2, 3, 4, 5, 10, 15, 20, 25, 50, or more codons) of the nativesequence with codons that are more frequently or most frequently used inthe genes of that host cell while maintaining the native amino acidsequence. Various species exhibit particular bias for certain codons ofa particular amino acid. Codon bias (differences in codon usage betweenorganisms) often correlates with the efficiency of translation ofmessenger RNA (mRNA), which is in turn believed to be dependent on,among other things, the properties of the codons being translated andthe availability of particular transfer RNA (tRNA) molecules. Thepredominance of selected tRNAs in a cell is generally a reflection ofthe codons used most frequently in peptide synthesis. Accordingly, genescan be tailored for optimal gene expression in a given organism based oncodon optimization. Codon usage tables are readily available, forexample, at the “Codon Usage Database” available atwww.kazusa.orjp/codon/ (visited Jul. 9, 2002), and these tables can beadapted in a number of ways. See Nakamura, Y., et al. “Codon usagetabulated from the international DNA sequence databases: status for theyear 2000” Nucl. Acids Res. 28:292 (2000). Computer algorithms for codonoptimizing a particular sequence for expression in a particular hostcell are also available, such as Gene Forge (Aptagen; Jacobus, Pa.), arealso available. In some embodiments, one or more codons (e.g. 1, 2, 3,4, 5, 10, 15, 20, 25, 50, or more, or all codons) in a sequence encodinga CRISPR enzyme correspond to the most frequently used codon for aparticular amino acid.

In some embodiments, a vector encodes a CRISPR enzyme comprising one ormore nuclear localization sequences (NLSs), such as about or more thanabout 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs. In some embodiments,the CRISPR enzyme comprises about or more than about 1, 2, 3, 4, 5, 6,7, 8, 9, 10, or more NLSs at or near the amino-terminus, about or morethan about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or near thecarboxy-terminus, or a combination of these (e.g. one or more NLS at theamino-terminus and one or more NLS at the carboxy terminus). When morethan one NLS is present, each may be selected independently of theothers, such that a single NLS may be present in more than one copyand/or in combination with one or more other NLSs present in one or morecopies. In a preferred embodiment of the invention, the CRISPR enzymecomprises at most 6 NLSs. In some embodiments, an NLS is considered nearthe N- or C-terminus when the nearest amino acid of the NLS is withinabout 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50, or more amino acidsalong the polypeptide chain from the N- or C-terminus. Non-limitingexamples of NLSs include an NLS sequence derived from: the NLS of theSV40 virus large T-antigen, having the amino acid sequence PKKKRKV; theNLS from nucleoplasmin (e.g. the nucleoplasmin bipartite NLS with thesequence KRPAATKKAGQAKKKK); the c-myc NLS having the amino acid sequencePAAKRVKLD or RQRRNELKRSP; the hRNPA1 M9 NLS having the sequenceNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY; the sequenceRMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV of the IBB domain fromimportin-alpha; the sequences VSRKRPRP and PPKKARED of the myoma Tprotein; the sequence POPKKKPL of human p53; the sequence SALIKKKKKMAPof mouse c-abl IV; the sequences DRLRR and PKQKKRK of the influenzavirus NS1; the sequence RKLKKKIKKL of the Hepatitis virus delta antigen;the sequence REKKKFLKRR of the mouse Mx1 protein; the sequenceKRKGDEVDGVDEVAKKKSKK of the human poly(ADP-ribose) polymerase; and thesequence RKCLQAGMNLEARKTKK of the steroid hormone receptors (human)glucocorticoid.

In general, the one or more N LSs are of sufficient strength to driveaccumulation of the CRISPR enzyme in a detectable amount in the nucleusof a eukaryotic cell. In general, strength of nuclear localizationactivity may derive from the number of NLSs in the CRISPR enzyme, theparticular NLS(s) used, or a combination of these factors. Detection ofaccumulation in the nucleus may be performed by any suitable technique.For example, a detectable marker may be fused to the CRISPR enzyme, suchthat location within a cell may be visualized, such as in combinationwith a means for detecting the location of the nucleus (e.g. a stainspecific for the nucleus such as DAPI). Cell nuclei may also be isolatedfrom cells, the contents of which may then be analyzed by any suitableprocess for detecting protein, such as immunohistochemistry, Westernblot, or enzyme activity assay. Accumulation in the nucleus may also bedetermined indirectly, such as by an assay for the effect of CRISPRcomplex formation (e.g. assay for DNA cleavage or mutation at the targetsequence, or assay for altered gene expression activity affected byCRISPR complex formation and/or CRISPR enzyme activity), as compared toa control no exposed to the CRISPR enzyme or complex, or exposed to aCRISPR enzyme lacking the one or more NLSs.

In general, a guide sequence is any polynucleotide sequence havingsufficient complementarity with a target polynucleotide sequence tohybridize with the target sequence and direct sequence-specific bindingof a CRISPR complex to the target sequence. In some embodiments, thedegree of complementarity between a guide sequence and its correspondingtarget sequence, when optimally aligned using a suitable alignmentalgorithm, is about or more than about 50%, 60%, 75%, 80%, 85%, 90%,95%, 97.5%, 99%, or more. Optimal alignment may be determined with theuse of any suitable algorithm for aligning sequences, non-limitingexample of which include the Smith-Waterman algorithm, theNeedleman-Wunsch algorithm, algorithms based on the Burrows-WheelerTransform (e.g. the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT,Novoalign (Novocraft Technologies; available at www.novocraf.com), ELAND(Illumina, San Diego, Calif.), SOAP (available at soap.genomics.org.cn),and Maq (available at maq.sourceforge.net). In some embodiments, a guidesequence is about or more than about 5, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 75,or more nucleotides in length. In some embodiments, a guide sequence isless than about 75, 50, 45, 40, 35, 30, 25, 20, 15, 12, or fewernucleotides in length. The ability of a guide sequence to directsequence-specific binding of a CRISPR complex to a target sequence maybe assessed by any suitable assay. For example, the components of aCRISPR system sufficient to form a CRISPR complex, including the guidesequence to be tested, may be provided to a host cell having thecorresponding target sequence, such as by transfection with vectorsencoding the components of the CRISPR sequence, followed by anassessment of preferential cleavage within the target sequence, such asby Surveyor assay as described herein. Similarly, cleavage of a targetpolynucleotide sequence may be evaluated in a test tube by providing thetarget sequence, components of a CRISPR complex, including the guidesequence to be tested and a control guide sequence different from thetest guide sequence, and comparing binding or rate of cleavage at thetarget sequence between the test and control guide sequence reactions.Other assays are possible, and will occur to those skilled in the art.

A guide sequence may be selected to target any target sequence. In someembodiments, the target sequence is a sequence within a genome of acell. Exemplary target sequences include those that are unique in thetarget genome. For example, for the S. pyogenes Cas9, a unique targetsequence in a genome may include a Cas9 target site of the formMMMMMMMMNNNNNNNNNNNNXGG where NNNNNNNNNNNNXGG (N is A, G, T, or C; and Xcan be anything) has a single occurrence in the genome. A unique targetsequence in a genome may include an S. pyogenes Cas9 target site of theform MMMMMMMMMNNNNNNNNNNNXGG where NNNNNNNNNNNXGG (N is A, G, T, or C;and X can be anything) has a single occurrence in the genome. For the S.thermophilus CRISPR1 Cas9, a unique target sequence in a genome mayinclude a Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNXXAGAAW whereNNNNNNNNNNNNXXAGAAW (N is A, G, T, or C; X can be anything; and W is Aor T) has a single occurrence in the genome. A unique target sequence ina genome may include an S. thermophilus CRISPR1Cas9 target site of theform MMMMMMMMMNNNNNNNNNNNXXAGAAW where NNNNNNNNNNNXXAGAAW (N is A, G, T,or C; X can be anything; and W is A or T) has a single occurrence in thegenome. For the S. pyogenes Cas9, a unique target sequence in a genomemay include a Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNXGGXGwhere NNNNNNNNNNNNXGGXG (N is A, G, T, or C; and X can be anything) hasa single occurrence in the genome. A unique target sequence in a genomemay include an S. pyogenes Cas9 target site of the formMMMMMMMMMNNNNNNNNNNNXGGXG where NNNNNNNNNNNXGGXG (N is A, G, T, or C;and X can be anything) has a single occurrence in the genome. In each ofthese sequences “M” may be A, G, T, or C, and need not be considered inidentifying a sequence as unique.

In some embodiments, a guide sequence is selected to reduce the degreeof secondary structure within the guide sequence. In some embodiments,about or less than about 75%, 50%, 40%, 30%, 25%, 20%, 15%, 10%, 5%, 1%,or fewer of the nucleotides of the guide sequence participate inself-complementary base pairing when optimally folded. Optimal foldingmay be determined by any suitable polynucleotide folding algorithm. Someprograms are based on calculating the minimal Gibbs free energy. Anexample of one such algorithm is mFold, as described by Zuker andStiegler (Nucleic Acids Res. 9 (1981), 133-148). Another example foldingalgorithm is the online webserver RNAfold, developed at Institute forTheoretical Chemistry at the University of Vienna, using the centroidstructure prediction algorithm (see e.g. A. R. Gruber et al., 2008, Cell106(1): 23-24; and P A Carr and G M Church, 2009, Nature Biotechnology27(12): 1151-62).

In general, a tracr mate sequence includes any sequence that hassufficient complementarity with a tracr sequence to promote one or moreof: (1) excision of a guide sequence flanked by tracr mate sequences ina cell containing the corresponding tracr sequence; and (2) formation ofa CRISPR complex at a target sequence, wherein the CRISPR complexcomprises the tracr mate sequence hybridized to the tracr sequence. Ingeneral, degree of complementarity is with reference to the optimalalignment of the tracr mate sequence and tracr sequence, along thelength of the shorter of the two sequences. Optimal alignment may bedetermined by any suitable alignment algorithm, and may further accountfor secondary structures, such as self-complementarity within either thetracr sequence or tracr mate sequence. In some embodiments, the degreeof complementarity between the tracr sequence and tracr mate sequencealong the length of the shorter of the two when optimally aligned isabout or more than about 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%,97.5%, 99%, or higher. In some embodiments, the tracr sequence is aboutor more than about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 25, 30, 40, 50, or more nucleotides in length. In someembodiments, the tracr sequence and tracr mate sequence are containedwithin a single transcript, such that hybridization between the twoproduces a transcript having a secondary structure, such as a hairpin.In an embodiment of the invention, the transcript or transcribedpolynucleotide sequence has at least two or more hairpins. In preferredembodiments, the transcript has two, three, four or five hairpins. In afurther embodiment of the invention, the transcript has at most fivehairpins. In a hairpin structure the portion of the sequence 5′ of thefinal “N” and upstream of the loop corresponds to the tracr matesequence, and the portion of the sequence 3′ of the loop corresponds tothe tracr sequence Further non-limiting examples of singlepolynucleotides comprising a guide sequence, a tracr mate sequence, anda tracr sequence are as follows (listed 5′ to 3′), where “N” representsa base of a guide sequence, the first block of lower case lettersrepresent the tracr mate sequence, and the second block of lower caseletters represent the tracr sequence, and the final poly-T sequencerepresents the transcription terminator:

(1) NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaagatttaGAAAtaaatcttgcagaagctacaaagataaggcttcatgccgaaatcaacaccctgtcattttatggcagggtgttttcgttatttaaTTTTTT; (2)NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaGAAAtgcagaagctacaaagataaggcttcatgccgaaatcaacaccctgtcattttatggcagggtgttttcgttatttaaTTTTT; (3)NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaGAAAtgcagaagctacaaagataaggcttcatgccgaaatcaacaccctgtcatttt atggcagggtgtTTTTTT; (4)NNNNNNNNNNNNNNNNNNNNgttttagagctaGAAAtagcaagttaaaataaggctagtccgttatcaacttgaaaaagtggcaccgagtcg gtgcTTTTT; (5)NNNNNNNNNNNNNNNNNNNNgttttagagctaGAAATAGcaagttaaaataaggctagtccgttatcaacttgaaaaagtgTTTTTTT; and (6)NNNNNNNNNNNNNNNNNNNNgttttagagctagAAATAGcaagttaaaataaggctagtccgttatcaTTTTTTTT.

In some embodiments, sequences (1) to (3) are used in combination withCas9 from S. thermophilus CRISPR1. In some embodiments, sequences (4) to(6) are used in combination with Cas9 from S. pyogenes. In someembodiments, the tracr sequence is a separate transcript from atranscript comprising the tracr mate sequence.

In some embodiments, a recombination template is also provided. Arecombination template may be a component of another vector as describedherein, contained in a separate vector, or provided as a separatepolynucleotide. In some embodiments, a recombination template isdesigned to serve as a template in homologous recombination, such aswithin or near a target sequence nicked or cleaved by a CRISPR enzyme asa part of a CRISPR complex. A template polynucleotide may be of anysuitable length, such as about or more than about 10, 15, 20, 25, 50,75, 100, 150, 200, 500, 1000, or more nucleotides in length. In someembodiments, the template polynucleotide is complementary to a portionof a polynucleotide comprising the target sequence. When optimallyaligned, a template polynucleotide might overlap with one or morenucleotides of a target sequences (e.g. about or more than about 1, 5,10, 15, 20, or more nucleotides). In some embodiments, when a templatesequence and a polynucleotide comprising a target sequence are optimallyaligned, the nearest nucleotide of the template polynucleotide is withinabout 1, 5, 10, 15, 20, 25, 50, 75, 100, 200, 300, 400, 500, 1000, 5000,10000, or more nucleotides from the target sequence.

In some embodiments, the CRISPR enzyme is part of a fusion proteincomprising one or more heterologous protein domains (e.g. about or morethan about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more domains in addition tothe CRISPR enzyme). A CRISPR enzyme fusion protein may comprise anyadditional protein sequence, and optionally a linker sequence betweenany two domains. Examples of protein domains that may be fused to aCRISPR enzyme include, without limitation, epitope tags, reporter genesequences, and protein domains having one or more of the followingactivities: methylase activity, demethylase activity, transcriptionactivation activity, transcription repression activity, transcriptionrelease factor activity, histone modification activity, RNA cleavageactivity and nucleic acid binding activity. Non-limiting examples ofepitope tags include histidine (His) tags, V5 tags, FLAG tags, influenzahemagglutinin (HA) tags, Myc tags, VSV-G tags, and thioredoxin (Trx)tags. Examples of reporter genes include, but are not limited to,glutathione-S-transferase (GST), horseradish peroxidase (HRP),chloramphenicol acetyltransferase (CAT) beta-galactosidase,beta-glucuronidase, luciferase, green fluorescent protein (GFP), HcRed,DsRed, cyan fluorescent protein (CFP), yellow fluorescent protein (YFP),and autofluorescent proteins including blue fluorescent protein (BFP). ACRISPR enzyme may be fused to a gene sequence encoding a protein or afragment of a protein that bind DNA molecules or bind other cellularmolecules, including but not limited to maltose binding protein (MBP),S-tag, Lex A DNA binding domain (DBD) fusions, GAL4A DNA binding domainfusions, and herpes simplex virus (HSV) BP16 protein fusions. Additionaldomains that may form part of a fusion protein comprising a CRISPRenzyme are described in US20110059502, incorporated herein by reference.In some embodiments, a tagged CRISPR enzyme is used to identify thelocation of a target sequence.

In some embodiments, a CRISPR enzyme may form a component of aninducible system. The inducible nature of the system would allow forspatiotemporal control of gene editing or gene expression using a formof energy. The form of energy may include but is not limited toelectromagnetic radiation, sound energy, chemical energy and thermalenergy. Examples of inducible system include tetracycline induciblepromoters (Tet-On or Tet-Off), small molecule two-hybrid transcriptionactivations systems (FKBP, ABA, etc), or light inducible systems(Phytochrome, LOV domains, or cryptochrome). In one embodiment, theCRISPR enzyme may be a part of a Light Inducible TranscriptionalEffector (LITE) to direct changes in transcriptional activity in asequence-specific manner. The components of a light may include a CRISPRenzyme, a light-responsive cytochrome heterodimer (e.g. from Arabidopsisthaliana), and a transcriptional activation/repression domain. Furtherexamples of inducible DNA binding proteins and methods for their use areprovided in U.S. 61/736,465 and U.S. 61/721,283, which is herebyincorporated by reference in its entirety.

In some aspects, the invention provides methods comprising deliveringone or more polynucleotides, such as or one or more vectors as describedherein, one or more transcripts thereof, and/or one or proteinstranscribed therefrom, to a host cell. In some aspects, the inventionfurther provides cells produced by such methods, and animals comprisingor produced from such cells. In some embodiments, a CRISPR enzyme incombination with (and optionally complexed with) a guide sequence isdelivered to a cell. Conventional viral and non-viral based genetransfer methods can be used to introduce nucleic acids in mammaliancells or target tissues. Such methods can be used to administer nucleicacids encoding components of a CRISPR system to cells in culture, or ina host organism. Non-viral vector delivery systems include DNA plasmids,RNA (e.g. a transcript of a vector described herein), naked nucleicacid, and nucleic acid complexed with a delivery vehicle, such as aliposome. Viral vector delivery systems include DNA and RNA viruses,which have either episomal or integrated genomes after delivery to thecell. For a review of gene therapy procedures, see Anderson, Science256:808-813 (1992); Nabel & Felgner, TIBTECH 11:211-217 (1993); Mitani &Caskey, TIBTECH 11:162-166 (1993); Dillon, TIBTECH 11:167-175 (1993);Miller, Nature 357:455-460 (1992); Van Brunt, Biotechnology6(10):1149-1154 (1988); Vigne, Restorative Neurology and Neuroscience8:35-36 (1995); Kremer & Perricaudet, British Medical Bulletin51(1):31-44 (1995); Haddada et al., in Current Topics in Microbiologyand Immunology Doerfler and Böhm (eds) (1995); and Yu et al., GeneTherapy 1:13-26 (1994).

Methods of non-viral delivery of nucleic acids include lipofection,microinjection, biolistics, virosomes, liposomes, immunoliposomes,polycation or lipid:nucleic acid conjugates, naked DNA, artificialvirions, and agent-enhanced uptake of DNA. Lipofection is described ine.g., U.S. Pat. Nos. 5,049,386, 4,946,787; and 4,897,355) andlipofection reagents are sold commercially (e.g., Transfectam™ andLipofectin™). Cationic and neutral lipids that are suitable forefficient receptor-recognition lipofection of polynucleotides includethose of Felgner, WO 91/17424; WO 91/16024. Delivery can be to cells(e.g. in vitro or ex vivo administration) or target tissues (e.g. invivo administration).

The preparation of lipid:nucleic acid complexes, including targetedliposomes such as immunolipid complexes, is well known to one of skillin the art (see, e.g., Crystal, Science 270:404-410 (1995); Blaese etal., Cancer Gene Ther. 2:291-297 (1995); Behr et al., Bioconjugate Chem.5:382-389 (1994); Remy et al., Bioconjugate Chem. 5:647-654 (1994); Gaoet al., Gene Therapy 2:710-722 (1995); Ahmad et al., Cancer Res.52:4817-4820 (1992); U.S. Pat. Nos. 4,186,183, 4,217,344, 4,235,871,4,261,975, 4,485,054, 4,501,728, 4,774,085, 4,837,028, and 4,946,787).

The use of RNA or DNA viral based systems for the delivery of nucleicacids take advantage of highly evolved processes for targeting a virusto specific cells in the body and trafficking the viral payload to thenucleus. Viral vectors can be administered directly to patients (invivo) or they can be used to treat cells in vitro, and the modifiedcells may optionally be administered to patients (ex vivo). Conventionalviral based systems could include retroviral, lentivirus, adenoviral,adeno-associated and herpes simplex virus vectors for gene transfer.Integration in the host genome is possible with the retrovirus,lentivirus, and adeno-associated virus gene transfer methods, oftenresulting in long term expression of the inserted transgene.Additionally, high transduction efficiencies have been observed in manydifferent cell types and target tissues.

The tropism of a retrovirus can be altered by incorporating foreignenvelope proteins, expanding the potential target population of targetcells. Lentiviral vectors are retroviral vectors that are able totransduce or infect non-dividing cells and typically produce high viraltiters. Selection of a retroviral gene transfer system would thereforedepend on the target tissue. Retroviral vectors are comprised ofcis-acting long terminal repeats with packaging capacity for up to 6-10kb of foreign sequence. The minimum cis-acting LTRs are sufficient forreplication and packaging of the vectors, which are then used tointegrate the therapeutic gene into the target cell to provide permanenttransgene expression. Widely used retroviral vectors include those basedupon murine leukemia virus (MuLV), gibbon ape leukemia virus (GaLV),Simian Immuno deficiency virus (SIV), human immuno deficiency virus(HIV), and combinations thereof (see, e.g., Buchscher et al., J. Virol.66:2731-2739 (1992); Johann et al., J. Virol. 66:1635-1640 (1992);Sommnerfelt et al., Virol. 176:58-59 (1990); Wilson et al., J. Virol.63:2374-2378 (1989); Miller et al., J. Virol. 65:2220-2224 (1991);PCT/US94/05700).

In another embodiment, Cocal vesiculovirus envelope pseudotypedretroviral vector particles are contemplated (see, e.g., US PatentPublication No. 20120164118 assigned to the Fred Hutchinson CancerResearch Center). Cocal virus is in the Vesiculovirus genus, and is acausative agent of vesicular stomatitis in mammals. Cocal virus wasoriginally isolated from mites in Trinidad (Jonkers et al., Am. J. Vet.Res. 25:236-242 (1964)), and infections have been identified inTrinidad, Brazil, and Argentina from insects, cattle, and horses. Manyof the vesiculoviruses that infect mammals have been isolated fromnaturally infected arthropods, suggesting that they are vector-borne.Antibodies to vesiculoviruses are common among people living in ruralareas where the viruses are endemic and laboratory-acquired; infectionsin humans usually result in influenza-like symptoms. The Cocal virusenvelope glycoprotein shares 71.5% identity at the amino acid level withVSV-G Indiana, and phylogenetic comparison of the envelope gene ofvesiculoviruses shows that Cocal virus is serologically distinct from,but most closely related to, VSV-G Indiana strains among thevesiculoviruses. Jonkers et al., Am. J. Vet. Res. 25:236-242 (1964) andTravassos da Rosa et al., Am. J. Tropical Med. & Hygiene 33:999-1006(1984). The Cocal vesiculovirus envelope pseudotyped retroviral vectorparticles may include for example, lentiviral, alpharetroviral,betaretroviral, gammaretroviral, deltaretroviral, and epsilonretroviralvector particles that may comprise retroviral Gag, Pol, and/or one ormore accessory protein(s) and a Cocal vesiculovirus envelope protein.Within certain aspects of these embodiments, the Gag, Pol, and accessoryproteins are lentiviral and/or gammaretroviral.

In applications where transient expression is preferred, adenoviralbased systems may be used. Adenoviral based vectors are capable of veryhigh transduction efficiency in many cell types and do not require celldivision. With such vectors, high titer and levels of expression havebeen obtained. This vector can be produced in large quantities in arelatively simple system. Adeno-associated virus (“AAV”) vectors mayalso be used to transduce cells with target nucleic acids, e.g., in thein vitro production of nucleic acids and peptides, and for in vivo andex vivo gene therapy procedures (see, e.g., West et al., Virology160:38-47 (1987); U.S. Pat. No. 4,797,368; WO 93/24641; Kotin, HumanGene Therapy 5:793-801 (1994); Muzyczka, J. Clin. Invest. 94:1351(1994). Construction of recombinant AAV vectors are described in anumber of publications, including U.S. Pat. No. 5,173,414; Tratschin etal., Mol. Cell. Biol. 5:3251-3260 (1985); Tratschin, et al., Mol. Cell.Biol. 4:2072-2081 (1984); Hermonat & Muzyczka, PNAS 81:6466-6470 (1984);and Samulski et al., J. Virol. 63:03822-3828 (1989).

Packaging cells are typically used to form virus particles that arecapable of infecting a host cell. Such cells include 293 cells, whichpackage adenovirus, and ψ2 cells or PA317 cells, which packageretrovirus. Viral vectors used in gene therapy are usually generated byproducer a cell line that packages a nucleic acid vector into a viralparticle. The vectors typically contain the minimal viral sequencesrequired for packaging and subsequent integration into a host, otherviral sequences being replaced by an expression cassette for thepolynucleotide(s) to be expressed. The missing viral functions aretypically supplied in trans by the packaging cell line. For example, AAVvectors used in gene therapy typically only possess ITR sequences fromthe AAV genome which are required for packaging and integration into thehost genome. Viral DNA is packaged in a cell line, which contains ahelper plasmid encoding the other AAV genes, namely rep and cap, butlacking ITR sequences. The cell line may also infected with adenovirusas a helper. The helper virus promotes replication of the AAV vector andexpression of AAV genes from the helper plasmid. The helper plasmid isnot packaged in significant amounts due to a lack of ITR sequences.Contamination with adenovirus can be reduced by, e.g., heat treatment towhich adenovirus is more sensitive than AAV.

Accordingly, AAV is considered an ideal candidate for use as atransducing vector. Such AAV transducing vectors can comprise sufficientcis-acting functions to replicate in the presence of adenovirus orherpesvirus or poxvirus (e.g., vaccinia virus) helper functions providedin trans. Recombinant AAV (rAAV) can be used to carry exogenous genesinto cells of a variety of lineages. In these vectors, the AAV capand/or rep genes are deleted from the viral genome and replaced with aDNA segment of choice. Current AAV vectors may accommodate up to 4300bases of inserted DNA.

There are a number of ways to produce rAAV, and the invention providesrAAV and methods for preparing rAAV. For example, plasmid(s) containingor consisting essentially of the desired viral construct are transfectedinto AAV-infected cells. In addition, a second or additional helperplasmid is cotransfected into these cells to provide the AAV rep and/orcap genes which are obligatory for replication and packaging of therecombinant viral construct. Under these conditions, the rep and/or capproteins of AAV act in trans to stimulate replication and packaging ofthe rAAV construct. Two to Three days after transfection, rAAV isharvested. Traditionally rAAV is harvested from the cells along withadenovirus. The contaminating adenovirus is then inactivated by heattreatment. In the instant invention, rAAV is advantageously harvestednot from the cells themselves, but from cell supernatant. Accordingly,in an initial aspect the invention provides for preparing rAAV, and inaddition to the foregoing, rAAV can be prepared by a method thatcomprises or consists essentially of: infecting susceptible cells with arAAV containing exogenous DNA including DNA for expression, and helpervirus (e.g., adenovirus, herpesvirus, poxvirus such as vaccinia virus)wherein the rAAV lacks functioning cap and/or rep (and the helper virus(e.g., adenovirus, herpesvirus, poxvirus such as vaccinia virus)provides the cap and/or rev function that the rAAV lacks); or infectingsusceptible cells with a rAAV containing exogenous DNA including DNA forexpression, wherein the recombinant lacks functioning cap and/or rep,and transfecting said cells with a plasmid supplying cap and/or repfunction that the rAAV lacks; or infecting susceptible cells with a rAAVcontaining exogenous DNA including DNA for expression, wherein therecombinant lacks functioning cap and/or rep, wherein said cells supplycap and/or rep function that the recombinant lacks; or transfecting thesusceptible cells with an AAV lacking functioning cap and/or rep andplasmids for inserting exogenous DNA into the recombinant so that theexogenous DNA is expressed by the recombinant and for supplying repand/or cap functions whereby transfection results in an rAAV containingthe exogenous DNA including DNA for expression that lacks functioningcap and/or rep.

The rAAV can be from an AAV as herein described, and advantageously canbe an rAAV1, rAAV2, AAV5 or rAAV having hybrid or capsid which maycomprise AAV1, AAV2, AAV5 or any combination thereof. One can select theAAV of the rAAV with regard to the cells to be targeted by the rAAV;e.g., one can select AAV serotypes 1, 2, 5 or a hybrid or capsid AAV1,AAV2, AAV5 or any combination thereof for targeting brain or neuronalcells; and one can select AAV4 for targeting cardiac tissue.

In addition to 293 cells, other cells that can be used in the practiceof the invention and the relative infectivity of certain AAV serotypesin vitro as to these cells (see Grimm. D. et al, J. Virol. 82: 5887-5911(2008)) are as follows:

Cell Line AAV-1 AAV-2 AAV-3 AAV-4 AAV-5 AAV-6 AAV-8 AAV-9 Huh-7 13 1002.5 0.0 0.1 10 0.7 0.0 HEK293 25 100 2.5 0.1 0.1 5 0.7 0.1 HeLa 3 1002.0 0.1 6.7 1 0.2 0.1 HepG2 3 100 16.7 0.3 1.7 5 0.3 ND Hep1A 20 100 0.21.0 0.1 1 0.2 0.0 911 17 100 11 0.2 0.1 17 0.1 ND CHO 100 100 14 1.4 33350 10 1.0 COS 33 100 33 3.3 5.0 14 2.0 0.5 MeWo 10 100 20 0.3 6.7 10 1.00.2 NIH3T3 10 100 2.9 2.9 0.3 10 0.3 ND A549 14 100 20 ND 0.5 10 0.5 0.1HT1180 20 100 10 0.1 0.3 33 0.5 0.1 Monocytes 1111 100 ND ND 125 1429 NDND Immature DC 2500 100 ND ND 222 2857 ND ND Mature DC 2222 100 ND ND333 3333 ND ND

The invention provides rAAV that contains or consists essentially of anexogenous nucleic acid molecule encoding a CRISPR (Clustered RegularlyInterspaced Short Palindromic Repeats) system, e.g., a plurality ofcassettes comprising or consisting a first cassette comprising orconsisting essentially of a promoter, a nucleic acid molecule encoding aCRISPR-associated (Cas) protein (putative nuclease or helicaseproteins), e.g., Cas9 and a terminator, and a two, or more,advantageously up to the packaging size limit of the vector, e.g., intotal (including the first cassette) five, cassettes comprising orconsisting essentially of a promoter, nucleic acid molecule encodingguide RNA (gRNA) and a terminator (e.g., each cassette schematicallyrepresented as Promoter-gRNA1-terminator, Promoter-gRNA2-terminator . .. Promoter-gRNA(N)-terminator (where N is a number that can be insertedthat is at an upper limit of the packaging size limit of the vector), ortwo or more individual rAAVs, each containing one or more than onecassette of a CRISPR system, e.g., a first rAAV containing the firstcassette comprising or consisting essentially of a promoter, a nucleicacid molecule encoding Cas, e.g., Cas9 and a terminator, and a secondrAAV containing a plurality, four, cassettes comprising or consistingessentially of a promoter, nucleic acid molecule encoding guide RNA(gRNA) and a terminator (e.g., each cassette schematically representedas Promoter-gRNA1-terminator, Promoter-gRNA2-terminator . . .Promoter-gRNA(N)-terminator (where N is a number that can be insertedthat is at an upper limit of the packaging size limit of the vector). AsrAAV is a DNA virus, the nucleic acid molecules in the herein discussionconcerning AAV or rAAV are advantageously DNA. The promoter is in someembodiments advantageously human Synapsin I promoter (hSyn).

Additional methods for the delivery of nucleic acids to cells are knownto those skilled in the art. See, for example, US20030087817,incorporated herein by reference.

In some embodiments, a host cell is transiently or non-transientlytransfected with one or more vectors described herein. In someembodiments, a cell is transfected as it naturally occurs in a subject.In some embodiments, a cell that is transfected is taken from a subject.In some embodiments, the cell is derived from cells taken from asubject, such as a cell line. A wide variety of cell lines for tissueculture are known in the art. Examples of cell lines include, but arenot limited to, C8161, CCRF-CEM, MOLT, mIMCD-3, NHDF, HeLa-S3, Huh1,Huh4, Huh7, HUVEC, HASMC, HEKn, HEKa, MiaPaCell, Pane1, PC-3, TF1,CTLL-2, C1R, Rat6, CV1, RPTE, A10, T24, J82, A375, ARH-77, Calu1, SW480,SW620, SKOV3, SK-UT, CaCo2, P388D1, SEM-K2, WEHI-231, HB56, TIB55,Jurkat, J45.01, LRMB, Bcl-1, BC-3, IC21, DLD2, Raw264.7, NRK, NRK-52E,MRC5, MEF, Hep G2, HeLa B, HeLa T4, COS, COS-1, COS-6, COS-M6A, BS-C-1monkey kidney epithelial, BALB/3T3 mouse embryo fibroblast, 3T3 Swiss,3T3-L1, 132-d5 human fetal fibroblasts; 10.1 mouse fibroblasts, 293-T,3T3, 721, 9L, A2780, A2780ADR, A2780cis, A172, A20, A253, A431, A-549,ALC, B16, B35, BCP-1 cells, BEAS-2B, bEnd.3, BHK-21, BR 293, BxPC3,C3H-10T1/2, C6/36, Cal-27, CHO, CHO-7, CHO-IR, CHO-K1, CHO-K2, CHO-T,CHO Dhfr −/−, COR-L23, COR-L23/CPR, COR-L23/5010, COR-L23/R23, COS-7,COV-434, CML T1, CMT, CT26, D17, DH82, DU145, DuCaP, EL4, EM2, EM3,EMT6/AR1, EMT6/AR10.0, FM3, H1299, H69, HB54, HB55, HCA2, HEK-293, HeLa,Hepa1c1c7, HL-60, HMEC, HT-29, Jurkat, JY cells, K562 cells, Ku812,KCL22, KG1, KYO1, LNCap, Ma-Me1 1-48, MC-38, MCF-7, MCF-10A, MDA-MB-231,MDA-MB-468, MDA-MB-435, MDCK II, MDCK II, MOR/0.2R, MONO-MAC 6, MTD-1A,MyEnd, NCI-H69/CPR, NCI-H69/LX10, NCI-H69/LX20, NCI-H69/LX4, NIH-3T3,NALM-1, NW-145, OPCN/OPCT cell lines, Peer, PNT-1A/PNT 2, RenCa, RIN-5F,RMA/RMAS, Saos-2 cells, Sf-9, SkBr3, T2, T-47D, T84, THP1 cell line,U373, U87, U937, VCaP, Vero cells, WM39, WT-49, X63, YAC-1, YAR, andtransgenic varieties thereof. Cell lines are available from a variety ofsources known to those with skill in the art (see, e.g., the AmericanType Culture Collection (ATCC) (Manassus, Va.)). In some embodiments, acell transfected with one or more vectors described herein is used toestablish a new cell line comprising one or more vector-derivedsequences. In some embodiments, a cell transiently transfected with thecomponents of a CRISPR system as described herein (such as by transienttransfection of one or more vectors, or transfection with RNA), andmodified through the activity of a CRISPR complex, is used to establisha new cell line comprising cells containing the modification but lackingany other exogenous sequence. In some embodiments, cells transiently ornon-transiently transfected with one or more vectors described herein,or cell lines derived from such cells are used in assessing one or moretest compounds.

In some embodiments, one or more vectors described herein are used toproduce a non-human transgenic animal or transgenic plant. In someembodiments, the transgenic animal is a mammal, such as a mouse, rat, orrabbit. Methods for producing transgenic animals and plants are known inthe art, and generally begin with a method of cell transfection, such asdescribed herein.

In another embodiment, a fluid delivery device with an array of needles(see, e.g., US Patent Publication No. 20110230839 assigned to the FredHutchinson Cancer Research Center) may be contemplated for delivery ofCRISPR Cas to solid tissue. A device of US Patent Publication No.20110230839 for delivery of a fluid to a solid tissue may comprise aplurality of needles arranged in an array; a plurality of reservoirs,each in fluid communication with a respective one of the plurality ofneedles; and a plurality of actuators operatively coupled to respectiveones of the plurality of reservoirs and configured to control a fluidpressure within the reservoir. In certain embodiments each of theplurality of actuators may comprise one of a plurality of plungers, afirst end of each of the plurality of plungers being received in arespective one of the plurality of reservoirs, and in certain furtherembodiments the plungers of the plurality of plungers are operativelycoupled together at respective second ends so as to be simultaneouslydepressable. Certain still further embodiments may comprise a plungerdriver configured to depress all of the plurality of plungers at aselectively variable rate. In other embodiments each of the plurality ofactuators may comprise one of a plurality of fluid transmission lineshaving first and second ends, a first end of each of the plurality offluid transmission lines being coupled to a respective one of theplurality of reservoirs. In other embodiments the device may comprise afluid pressure source, and each of the plurality of actuators comprisesa fluid coupling between the fluid pressure source and a respective oneof the plurality of reservoirs. In further embodiments the fluidpressure source may comprise at least one of a compressor, a vacuumaccumulator, a peristaltic pump, a master cylinder, a microfluidic pump,and a valve. In another embodiment, each of the plurality of needles maycomprise a plurality of ports distributed along its length.

In one aspect, the invention provides for methods of modifying a targetpolynucleotide in a eukaryotic cell, which may be in vivo, ex vivo or invitro. In some embodiments, the method comprises sampling a cell orpopulation of cells from a human or non-human animal, or a plant, andmodifying the cell or cells. Culturing may occur at any stage ex vivo.The cell or cells may even be re-introduced into the non-human animal orplant. For re-introduced cells it is particularly preferred that thecells are stem cells.

In some embodiments, the method comprises allowing a CRISPR complex tobind to the target polynucleotide to effect cleavage of said targetpolynucleotide thereby modifying the target polynucleotide, wherein theCRISPR complex comprises a CRISPR enzyme complexed with a guide sequencehybridized to a target sequence within said target polynucleotide,wherein said guide sequence is linked to a tracr mate sequence which inturn hybridizes to a tracr sequence.

In one aspect, the invention provides a method of modifying expressionof a polynucleotide in a eukaryotic cell. In some embodiments, themethod comprises allowing a CRISPR complex to bind to the polynucleotidesuch that said binding results in increased or decreased expression ofsaid polynucleotide; wherein the CRISPR complex comprises a CRISPRenzyme complexed with a guide sequence hybridized to a target sequencewithin said polynucleotide, wherein said guide sequence is linked to atracr mate sequence which in turn hybridizes to a tracr sequence.Similar considerations and conditions apply as above for methods ofmodifying a target polynucleotide. In fact, these sampling, culturingand re-introduction options apply across the aspects of the presentinvention.

Indeed, in any aspect of the invention, the CRISPR complex may comprisea CRISPR enzyme complexed with a guide sequence hybridized to a targetsequence, wherein said guide sequence may be linked to a tracr matesequence which in turn may hybridize to a tracr sequence. Similarconsiderations and conditions apply as above for methods of modifying atarget polynucleotide.

In one aspect, the invention provides kits containing any one or more ofthe elements disclosed in the above methods and compositions. Elementsmay be provided individually or in combinations, and may be provided inany suitable container, such as a vial, a bottle, or a tube. In someembodiments, the kit includes instructions in one or more languages, forexample in more than one language.

In some embodiments, a kit comprises one or more reagents for use in aprocess utilizing one or more of the elements described herein. Reagentsmay be provided in any suitable container. For example, a kit mayprovide one or more reaction or storage buffers. Reagents may beprovided in a form that is usable in a particular assay, or in a formthat requires addition of one or more other components before use (e.g.in concentrate or lyophilized form). A buffer can be any buffer,including but not limited to a sodium carbonate buffer, a sodiumbicarbonate buffer, a borate buffer, a Tris buffer, a MOPS buffer, aHEPES buffer, and combinations thereof. In some embodiments, the bufferis alkaline. In some embodiments, the buffer has a pH from about 7 toabout 10. In some embodiments, the kit comprises one or moreoligonucleotides corresponding to a guide sequence for insertion into avector so as to operably link the guide sequence and a regulatoryelement. In some embodiments, the kit comprises a homologousrecombination template polynucleotide. In some embodiments, the kitcomprises one or more of the vectors and/or one or more of thepolynucleotides described herein. The kit may advantageously allows toprovide all elements of the systems of the invention.

In one aspect, the invention provides methods for using one or moreelements of a CRISPR system. The CRISPR complex of the inventionprovides an effective means for modifying a target polynucleotide. TheCRISPR complex of the invention has a wide variety of utility includingmodifying (e.g., deleting, inserting, translocating, inactivating,activating) a target polynucleotide in a multiplicity of cell types. Assuch the CRISPR complex of the invention has a broad spectrum ofapplications in, e.g., gene therapy, drug screening, disease diagnosis,and prognosis. An exemplary CRISPR complex comprises a CRISPR enzymecomplexed with a guide sequence hybridized to a target sequence withinthe target polynucleotide. The guide sequence is linked to a tracr matesequence, which in turn hybridizes to a tracr sequence.

In one embodiment, this invention provides a method of cleaving a targetpolynucleotide. The method comprises modifying a target polynucleotideusing a CRISPR complex that binds to the target polynucleotide andeffect cleavage of said target polynucleotide. Typically, the CRISPRcomplex of the invention, when introduced into a cell, creates a break(e.g., a single or a double strand break) in the genome sequence. Forexample, the method can be used to cleave a disease gene in a cell.

The break created by the CRISPR complex can be repaired by a repairprocesses such as the error prone non-homologous end joining (NHEJ)pathway or the high fidelity homology-directed repair (HDR) (FIG. 29).During these repair process, an exogenous polynucleotide template can beintroduced into the genome sequence. In some methods, the HDR process isused to modify the genome sequence. For example, an exogenouspolynucleotide template comprising a sequence to be integrated flankedby an upstream sequence and a downstream sequence is introduced into acell. The upstream and downstream sequences share sequence similaritywith either side of the site of integration in the chromosome.

Where desired, a donor polynucleotide can be DNA, e.g., a DNA plasmid, abacterial artificial chromosome (BAC), a yeast artificial chromosome(YAC), a viral vector, a linear piece of DNA, a PCR fragment, a nakednucleic acid, or a nucleic acid complexed with a delivery vehicle suchas a liposome or poloxamer.

The exogenous polynucleotide template comprises a sequence to beintegrated (e.g., a mutated gene). The sequence for integration may be asequence endogenous or exogenous to the cell. Examples of a sequence tobe integrated include polynucleotides encoding a protein or a non-codingRNA (e.g., a microRNA). Thus, the sequence for integration may beoperably linked to an appropriate control sequence or sequences.Alternatively, the sequence to be integrated may provide a regulatoryfunction.

The upstream and downstream sequences in the exogenous polynucleotidetemplate are selected to promote recombination between the chromosomalsequence of interest and the donor polynucleotide. The upstream sequenceis a nucleic acid sequence that shares sequence similarity with thegenome sequence upstream of the targeted site for integration.Similarly, the downstream sequence is a nucleic acid sequence thatshares sequence similarity with the chromosomal sequence downstream ofthe targeted site of integration. The upstream and downstream sequencesin the exogenous polynucleotide template can have 75%, 80%, 85%, 90%,95%, or 100% sequence identity with the targeted genome sequence.Preferably, the upstream and downstream sequences in the exogenouspolynucleotide template have about 95%, 96%, 97%, 98%, 99%, or 100%sequence identity with the targeted genome sequence. In some methods,the upstream and downstream sequences in the exogenous polynucleotidetemplate have about 99% or 100% sequence identity with the targetedgenome sequence.

An upstream or downstream sequence may comprise from about 20 bp toabout 2500 bp, for example, about 50, 100, 200, 300, 400, 500, 600, 700,800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900,2000, 2100, 2200, 2300, 2400, or 2500 bp. In some methods, the exemplaryupstream or downstream sequence have about 200 bp to about 2000 bp,about 600 bp to about 1000 bp, or more particularly about 700 bp toabout 1000 bp.

In some methods, the exogenous polynucleotide template may furthercomprise a marker. Such a marker may make it easy to screen for targetedintegrations. Examples of suitable markers include restriction sites,fluorescent proteins, or selectable markers. The exogenouspolynucleotide template of the invention can be constructed usingrecombinant techniques (see, for example, Sambrook et al., 2001 andAusubel et al., 1996).

In an exemplary method for modifying a target polynucleotide byintegrating an exogenous polynucleotide template, a double strandedbreak is introduced into the genome sequence by the CRISPR complex, thebreak is repaired via homologous recombination an exogenouspolynucleotide template such that the template is integrated into thegenome. The presence of a double-stranded break facilitates integrationof the template.

In other embodiments, this invention provides a method of modifyingexpression of a polynucleotide in a eukaryotic cell. The methodcomprises increasing or decreasing expression of a target polynucleotideby using a CRISPR complex that binds to the polynucleotide.

In some methods, a target polynucleotide can be inactivated to effectthe modification of the expression in a cell. For example, upon thebinding of a CRISPR complex to a target sequence in a cell, the targetpolynucleotide is inactivated such that the sequence is not transcribed,the coded protein is not produced, or the sequence does not function asthe wild-type sequence does. For example, a protein or microRNA codingsequence may be inactivated such that the protein is not produced.

In some methods, a control sequence can be inactivated such that it nolonger functions as a control sequence. As used herein, “controlsequence” refers to any nucleic acid sequence that effects thetranscription, translation, or accessibility of a nucleic acid sequence.Examples of a control sequence include, a promoter, a transcriptionterminator, and an enhancer are control sequences.

The inactivated target sequence may include a deletion mutation (i.e.,deletion of one or more nucleotides), an insertion mutation (i.e.,insertion of one or more nucleotides), or a nonsense mutation (i.e.,substitution of a single nucleotide for another nucleotide such that astop codon is introduced). In some methods, the inactivation of a targetsequence results in “knock-out” of the target sequence.

A method of the invention may be used to create a plant, an animal orcell that may be used as a disease model. As used herein, “disease”refers to a disease, disorder, or indication in a subject. For example,a method of the invention may be used to create an animal or cell thatcomprises a modification in one or more nucleic acid sequencesassociated with a disease, or a plant, animal or cell in which theexpression of one or more nucleic acid sequences associated with adisease are altered. Such a nucleic acid sequence may encode a diseaseassociated protein sequence or may be a disease associated controlsequence. Accordingly, it is understood that in embodiments of theinvention, a plant, subject, patient, organism or cell can be anon-human subject, patient, organism or cell. Thus, the inventionprovides a plant, animal or cell, produced by the present methods, or aprogeny thereof. The progeny may be a clone of the produced plant oranimal, or may result from sexual reproduction by crossing with otherindividuals of the same species to introgress further desirable traitsinto their offspring. The cell may be in vivo or ex vivo in the cases ofmulticellular organisms, particularly animals or plants. In the instancewhere the cell is in cultured, a cell line may be established ifappropriate culturing conditions are met and preferably if the cell issuitably adapted for this purpose (for instance a stem cell). Bacterialcell lines produced by the invention are also envisaged. Hence, celllines are also envisaged.

In some methods, the disease model can be used to study the effects ofmutations on the animal or cell and development and/or progression ofthe disease using measures commonly used in the study of the disease.Alternatively, such a disease model is useful for studying the effect ofa pharmaceutically active compound on the disease.

In some methods, the disease model can be used to assess the efficacy ofa potential gene therapy strategy. That is, a disease-associated gene orpolynucleotide can be modified such that the disease development and/orprogression is inhibited or reduced. In particular, the method comprisesmodifying a disease-associated gene or polynucleotide such that analtered protein is produced and, as a result, the animal or cell has analtered response. Accordingly, in some methods, a genetically modifiedanimal may be compared with an animal predisposed to development of thedisease such that the effect of the gene therapy event may be assessed.

In another embodiment, this invention provides a method of developing abiologically active agent that modulates a cell signaling eventassociated with a disease gene. The method comprises contacting a testcompound with a cell comprising one or more vectors that driveexpression of one or more of a CRISPR enzyme, a guide sequence linked toa tracr mate sequence, and a tracr sequence; and detecting a change in areadout that is indicative of a reduction or an augmentation of a cellsignaling event associated with, e.g., a mutation in a disease genecontained in the cell.

A cell model or animal model can be constructed in combination with themethod of the invention for screening a cellular function change. Such amodel may be used to study the effects of a genome sequence modified bythe CRISPR complex of the invention on a cellular function of interest.For example, a cellular function model may be used to study the effectof a modified genome sequence on intracellular signaling orextracellular signaling. Alternatively, a cellular function model may beused to study the effects of a modified genome sequence on sensoryperception. In some such models, one or more genome sequences associatedwith a signaling biochemical pathway in the model are modified.

Several disease models have been specifically investigated. Theseinclude de novo autism risk genes CHD8, KATNAL2, and SCN2A; and thesyndromic autism (Angelman Syndrome) gene UBE3A. These genes andresulting autism models are of course preferred, but serve to show thebroad applicability of the invention across genes and correspondingmodels.

An altered expression of one or more genome sequences associated with asignaling biochemical pathway can be determined by assaying for adifference in the mRNA levels of the corresponding genes between thetest model cell and a control cell, when they are contacted with acandidate agent. Alternatively, the differential expression of thesequences associated with a signaling biochemical pathway is determinedby detecting a difference in the level of the encoded polypeptide orgene product.

To assay for an agent-induced alteration in the level of mRNAtranscripts or corresponding polynucleotides, nucleic acid contained ina sample is first extracted according to standard methods in the art.For instance, mRNA can be isolated using various lytic enzymes orchemical solutions according to the procedures set forth in Sambrook etal. (1989), or extracted by nucleic-acid-binding resins following theaccompanying instructions provided by the manufacturers. The mRNAcontained in the extracted nucleic acid sample is then detected byamplification procedures or conventional hybridization assays (e.g.Northern blot analysis) according to methods widely known in the art orbased on the methods exemplified herein.

For purpose of this invention, amplification means any method employinga primer and a polymerase capable of replicating a target sequence withreasonable fidelity. Amplification may be carried out by natural orrecombinant DNA polymerases such as TaqGold™, T7 DNA polymerase, Klenowfragment of E. coli DNA polymerase, and reverse transcriptase. Apreferred amplification method is PCR. In particular, the isolated RNAcan be subjected to a reverse transcription assay that is coupled with aquantitative polymerase chain reaction (RT-PCR) in order to quantify theexpression level of a sequence associated with a signaling biochemicalpathway.

Detection of the gene expression level can be conducted in real time inan amplification assay. In one aspect, the amplified products can bedirectly visualized with fluorescent DNA-binding agents including butnot limited to DNA intercalators and DNA groove binders. Because theamount of the intercalators incorporated into the double-stranded DNAmolecules is typically proportional to the amount of the amplified DNAproducts, one can conveniently determine the amount of the amplifiedproducts by quantifying the fluorescence of the intercalated dye usingconventional optical systems in the art. DNA-binding dye suitable forthis application include SYBR green, SYBR blue, DAPI, propidium iodine,Hoeste, SYBR gold, ethidium bromide, acridines, proflavine, acridineorange, acriflavine, fluorcoumanin, ellipticine, daunomycin,chloroquine, distamycin D, chromomycin, homidium, mithramycin, rutheniumpolypyridyls, anthramycin, and the like.

In another aspect, other fluorescent labels such as sequence specificprobes can be employed in the amplification reaction to facilitate thedetection and quantification of the amplified products. Probe-basedquantitative amplification relies on the sequence-specific detection ofa desired amplified product. It utilizes fluorescent, target-specificprobes (e.g., TaqMan® probes) resulting in increased specificity andsensitivity. Methods for performing probe-based quantitativeamplification are well established in the art and are taught in U.S.Pat. No. 5,210,015.

In yet another aspect, conventional hybridization assays usinghybridization probes that share sequence homology with sequencesassociated with a signaling biochemical pathway can be performed.Typically, probes are allowed to form stable complexes with thesequences associated with a signaling biochemical pathway containedwithin the biological sample derived from the test subject in ahybridization reaction. It will be appreciated by one of skill in theart that where antisense is used as the probe nucleic acid, the targetpolynucleotides provided in the sample are chosen to be complementary tosequences of the antisense nucleic acids. Conversely, where thenucleotide probe is a sense nucleic acid, the target polynucleotide isselected to be complementary to sequences of the sense nucleic acid.

Hybridization can be performed under conditions of various stringency.Suitable hybridization conditions for the practice of the presentinvention are such that the recognition interaction between the probeand sequences associated with a signaling biochemical pathway is bothsufficiently specific and sufficiently stable. Conditions that increasethe stringency of a hybridization reaction are widely known andpublished in the art. See, for example, (Sambrook, et al., (1989);Nonradioactive In Situ Hybridization Application Manual, BoehringerMannheim, second edition). The hybridization assay can be formed usingprobes immobilized on any solid support, including but are not limitedto nitrocellulose, glass, silicon, and a variety of gene arrays. Apreferred hybridization assay is conducted on high-density gene chips asdescribed in U.S. Pat. No. 5,445,934.

For a convenient detection of the probe-target complexes formed duringthe hybridization assay, the nucleotide probes are conjugated to adetectable label. Detectable labels suitable for use in the presentinvention include any composition detectable by photochemical,biochemical, spectroscopic, immunochemical, electrical, optical orchemical means. A wide variety of appropriate detectable labels areknown in the art, which include fluorescent or chemiluminescent labels,radioactive isotope labels, enzymatic or other ligands. In preferredembodiments, one will likely desire to employ a fluorescent label or anenzyme tag, such as digoxigenin, β-galactosidase, urease, alkalinephosphatase or peroxidase, avidin/biotin complex.

The detection methods used to detect or quantify the hybridizationintensity will typically depend upon the label selected above. Forexample, radiolabels may be detected using photographic film or aphosphoimager. Fluorescent markers may be detected and quantified usinga photodetector to detect emitted light. Enzymatic labels are typicallydetected by providing the enzyme with a substrate and measuring thereaction product produced by the action of the enzyme on the substrate;and finally colorimetric labels are detected by simply visualizing thecolored label.

An agent-induced change in expression of sequences associated with asignaling biochemical pathway can also be determined by examining thecorresponding gene products. Determining the protein level typicallyinvolves a) contacting the protein contained in a biological sample withan agent that specifically bind to a protein associated with a signalingbiochemical pathway; and (b) identifying any agent:protein complex soformed. In one aspect of this embodiment, the agent that specificallybinds a protein associated with a signaling biochemical pathway is anantibody, preferably a monoclonal antibody.

The reaction is performed by contacting the agent with a sample of theproteins associated with a signaling biochemical pathway derived fromthe test samples under conditions that will allow a complex to formbetween the agent and the proteins associated with a signalingbiochemical pathway. The formation of the complex can be detecteddirectly or indirectly according to standard procedures in the art. Inthe direct detection method, the agents are supplied with a detectablelabel and unreacted agents may be removed from the complex; the amountof remaining label thereby indicating the amount of complex formed. Forsuch method, it is preferable to select labels that remain attached tothe agents even during stringent washing conditions. It is preferablethat the label does not interfere with the binding reaction. In thealternative, an indirect detection procedure may use an agent thatcontains a label introduced either chemically or enzymatically. Adesirable label generally does not interfere with binding or thestability of the resulting agent:polypeptide complex. However, the labelis typically designed to be accessible to an antibody for an effectivebinding and hence generating a detectable signal.

A wide variety of labels suitable for detecting protein levels are knownin the art. Non-limiting examples include radioisotopes, enzymes,colloidal metals, fluorescent compounds, bioluminescent compounds, andchemiluminescent compounds.

The amount of agent:polypeptide complexes formed during the bindingreaction can be quantified by standard quantitative assays. Asillustrated above, the formation of agent:polypeptide complex can bemeasured directly by the amount of label remained at the site ofbinding. In an alternative, the protein associated with a signalingbiochemical pathway is tested for its ability to compete with a labeledanalog for binding sites on the specific agent. In this competitiveassay, the amount of label captured is inversely proportional to theamount of protein sequences associated with a signaling biochemicalpathway present in a test sample.

A number of techniques for protein analysis based on the generalprinciples outlined above are available in the art. They include but arenot limited to radioimmunoassays, ELISA (enzyme linked immunoradiometricassays), “sandwich” immunoassays, immunoradiometric assays, in situimmunoassays (using e.g., colloidal gold, enzyme or radioisotopelabels), western blot analysis, immunoprecipitation assays,immunofluorescent assays, and SDS-PAGE.

Antibodies that specifically recognize or bind to proteins associatedwith a signaling biochemical pathway are preferable for conducting theaforementioned protein analyses. Where desired, antibodies thatrecognize a specific type of post-translational modifications (e.g.,signaling biochemical pathway inducible modifications) can be used.Post-translational modifications include but are not limited toglycosylation, lipidation, acetylation, and phosphorylation. Theseantibodies may be purchased from commercial vendors. For example,anti-phosphotyrosine antibodies that specifically recognizetyrosine-phosphorylated proteins are available from a number of vendorsincluding Invitrogen and Perkin Elmer. Anti-phosphotyrosine antibodiesare particularly useful in detecting proteins that are differentiallyphosphorylated on their tyrosine residues in response to an ER stress.Such proteins include but are not limited to eukaryotic translationinitiation factor 2 alpha (eIF-2α). Alternatively, these antibodies canbe generated using conventional polyclonal or monoclonal antibodytechnologies by immunizing a host animal or an antibody-producing cellwith a target protein that exhibits the desired post-translationalmodification.

In practicing the subject method, it may be desirable to discern theexpression pattern of an protein associated with a signaling biochemicalpathway in different bodily tissue, in different cell types, and/or indifferent subcellular structures. These studies can be performed withthe use of tissue-specific, cell-specific or subcellular structurespecific antibodies capable of binding to protein markers that arepreferentially expressed in certain tissues, cell types, or subcellularstructures.

An altered expression of a gene associated with a signaling biochemicalpathway can also be determined by examining a change in activity of thegene product relative to a control cell. The assay for an agent-inducedchange in the activity of a protein associated with a signalingbiochemical pathway will dependent on the biological activity and/or thesignal transduction pathway that is under investigation. For example,where the protein is a kinase, a change in its ability to phosphorylatethe downstream substrate(s) can be determined by a variety of assaysknown in the art. Representative assays include but are not limited toimmunoblotting and immunoprecipitation with antibodies such asanti-phosphotyrosine antibodies that recognize phosphorylated proteins.In addition, kinase activity can be detected by high throughputchemiluminescent assays such as AlphaScreen™ (available from PerkinElmer) and eTag™ assay (Chan-Hui, et al. (2003) Clinical Immunology 111:162-174).

Where the protein associated with a signaling biochemical pathway ispart of a signaling cascade leading to a fluctuation of intracellular pHcondition, pH sensitive molecules such as fluorescent pH dyes can beused as the reporter molecules. In another example where the proteinassociated with a signaling biochemical pathway is an ion channel,fluctuations in membrane potential and/or intracellular ionconcentration can be monitored. A number of commercial kits andhigh-throughput devices are particularly suited for a rapid and robustscreening for modulators of ion channels. Representative instrumentsinclude FLIPR™ (Molecular Devices, Inc.) and VIPR (Aurora Biosciences).These instruments are capable of detecting reactions in over 1000 samplewells of a microplate simultaneously, and providing real-timemeasurement and functional data within a second or even a minisecond.

In practicing any of the methods disclosed herein, a suitable vector canbe introduced to a cell or an embryo via one or more methods known inthe art, including without limitation, microinjection, electroporation,sonoporation, biolistics, calcium phosphate-mediated transfection,cationic transfection, liposome transfection, dendrimer transfection,heat shock transfection, nucleofection transfection, magnetofection,lipofection, impalefection, optical transfection, proprietaryagent-enhanced uptake of nucleic acids, and delivery via liposomes,immunoliposomes, virosomes, or artificial virions. In some methods, thevector is introduced into an embryo by microinjection. The vector orvectors may be microinjected into the nucleus or the cytoplasm of theembryo. In some methods, the vector or vectors may be introduced into acell by nucleofection.

The target polynucleotide of a CRISPR complex can be any polynucleotideendogenous or exogenous to the eukaryotic cell. For example, the targetpolynucleotide can be a polynucleotide residing in the nucleus of theeukaryotic cell. The target polynucleotide can be a sequence coding agene product (e.g., a protein) or a non-coding sequence (e.g., aregulatory polynucleotide or a junk DNA).

Examples of target polynucleotides include a sequence associated with asignaling biochemical pathway, e.g., a signaling biochemicalpathway-associated gene or polynucleotide. Examples of targetpolynucleotides include a disease associated gene or polynucleotide. A“disease-associated” gene or polynucleotide refers to any gene orpolynucleotide which is yielding transcription or translation productsat an abnormal level or in an abnormal form in cells derived from adisease-affected tissues compared with tissues or cells of a non diseasecontrol. It may be a gene that becomes expressed at an abnormally highlevel; it may be a gene that becomes expressed at an abnormally lowlevel, where the altered expression correlates with the occurrenceand/or progression of the disease. A disease-associated gene also refersto a gene possessing mutation(s) or genetic variation that is directlyresponsible or is in linkage disequilibrium with a gene(s) that isresponsible for the etiology of a disease. The transcribed or translatedproducts may be known or unknown, and may be at a normal or abnormallevel.

The target polynucleotide of a CRISPR complex can be any polynucleotideendogenous or exogenous to the eukaryotic cell. For example, the targetpolynucleotide can be a polynucleotide residing in the nucleus of theeukaryotic cell. The target polynucleotide can be a sequence coding agene product (e.g., a protein) or a non-coding sequence (e.g., aregulatory polynucleotide or a junk DNA). Without wishing to be bound bytheory, it is believed that the target sequence should be associatedwith a PAM (protospacer adjacent motif); that is, a short sequencerecognized by the CRISPR complex. The precise sequence and lengthrequirements for the PAM differ depending on the CRISPR enzyme used, butPAMs are typically 2-5 base pair sequences adjacent the protospacer(that is, the target sequence) Examples of PAM sequences are given inthe examples section below, and the skilled person will be able toidentify further PAM sequences for use with a given CRISPR enzyme.

The target polynucleotide of a CRISPR complex may include a number ofdisease-associated genes and polynucleotides as well as signalingbiochemical pathway-associated genes and polynucleotides as listed inU.S. provisional patent applications 61/736,527 and 61/748,427 havingBroad reference BI-2011/008/WSGR Docket No. 44063-701.101 andBI-2011/008/WSGR Docket No. 44063-701.102 respectively, both entitledSYSTEMS METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION filed on Dec.12, 2012 and Jan. 2, 2013, respectively, the contents of all of whichare herein incorporated by reference in their entirety.

Examples of target polynucleotides include a sequence associated with asignaling biochemical pathway, e.g., a signaling biochemicalpathway-associated gene or polynucleotide. Examples of targetpolynucleotides include a disease associated gene or polynucleotide. A“disease-associated” gene or polynucleotide refers to any gene orpolynucleotide which is yielding transcription or translation productsat an abnormal level or in an abnormal form in cells derived from adisease-affected tissues compared with tissues or cells of a non diseasecontrol. It may be a gene that becomes expressed at an abnormally highlevel; it may be a gene that becomes expressed at an abnormally lowlevel, where the altered expression correlates with the occurrenceand/or progression of the disease. A disease-associated gene also refersto a gene possessing mutation(s) or genetic variation that is directlyresponsible or is in linkage disequilibrium with a gene(s) that isresponsible for the etiology of a disease. The transcribed or translatedproducts may be known or unknown, and may be at a normal or abnormallevel.

Examples of disease-associated genes and polynucleotides are listed inTables A and B. Disease specific information is available fromMcKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University(Baltimore, Md.) and National Center for Biotechnology Information,National Library of Medicine (Bethesda, Md.), available on the WorldWide Web. Examples of signaling biochemical pathway-associated genes andpolynucleotides are listed in Table C.

Mutations in these genes and pathways can result in production ofimproper proteins or proteins in improper amounts which affect function.Further examples of genes, diseases and proteins are hereby incorporatedby reference from U.S. Provisional applications 61/736,527 filed Dec.12, 2012 and 61/748,427 filed on Jan. 2, 2013. Such genes, proteins andpathways may be the target polynucleotide of a CRISPR complex.

TABLE A DISEASE/DISORDERS GENE(S) Neoplasia PTEN; ATM; ATR; EGFR; ERBB2;ERBB3; ERBB4; Notch1; Notch2; Notch3; Notch4; AKT; AKT2; AKT3; HIF;HIF1a; HIF3a; Met; HRG; Bcl2; PPAR alpha; PPAR gamma; WT1 (Wilms Tumor);FGF Receptor Family members (5 members: 1, 2, 3, 4, 5); CDKN2a; APC; RB(retinoblastoma); MEN1; VHL; BRCA1; BRCA2; AR (Androgen Receptor);TSG101; IGF; IGF Receptor; Igf1(4 variants); Igf2 (3 variants); Igf 1Receptor; Igf 2 Receptor; Bax; Bcl2; caspases family (9 members: 1, 2,3, 4, 6, 7, 8, 9, 12); Kras; Apc Age-related Macular Abcr; Ccl2; Cc2; cp(ceruloplasmin); Timp3; cathepsinD; Degeneration Vldlr; Ccr2Schizophrenia Neuregulin1 (Nrg1); Erb4 (receptor for Neuregulin);Complexin1 (Cplx1); Tph1 Tryptophan hydroxylase; Tph2 Tryptophanhydroxylase 2; Neurexin 1; GSK3; GSK3a; GSK3b Disorders 5-HTT (Slc6a4);COMT; DRD (Drd1a); SLC6A3; DAOA; DTNBP1; Dao (Dao1) Trinucleotide RepeatHTT (Huntington's Dx); SBMA/SMAX1/AR (Kennedy's Disorders Dx); FXN/X25(Friedrich's Ataxia); ATX3 (Machado- Joseph's Dx); ATXN1 and ATXN2(spinocerebellar ataxias); DMPK (myotonic dystrophy); Atrophin-1 andAtn1 (DRPLA Dx); CBP (Creb-BP-global instability); VLDLR (Alzheimer's);Atxn7; Atxn10 Fragile X Syndrome FMR2; FXR1; FXR2; mGLUR5 SecretaseRelated APH-1 (alpha and beta); Presenilin (Psen1); nicastrin Disorders(Ncstn); PEN-2 Others Nos1; Parp1; Nat1; Nat2 Prion-related disordersPrp ALS SOD1; ALS2; STEX; FUS; TARDBP; VEGF (VEGF-a; VEGF-b; -VEGF-c)Drug addiction Prkce (alcohol); Drd2; Drd4; ABAT (alcohol); GRIA2; Grm5;Grin1; Htr1b; Grin2a; Drd3; Pdyn; Gria1 (alcohol) Autism Mecp2; BZRAP1;MDGA2; Sema5A; Neurexin 1; Fragile X (FMR2 (AFF2); FXR1; FXR2; Mglur5)Alzheimer's Disease E1; CHIP; UCH; UBB; Tau; LRP; PICALM; Clusterin;PS1; SORL1; CR1; Vldlr; Uba1; Uba3; CHIP28 (Aqp1, Aquaporin 1); Uchl1;Urhl3; APP Inflammation IL-10; IL-1 (IL-1a; IL-1b); IL-13; IL-17 (IL-17a(CTLA8); IL- 17b; IL-17c; IL-17d; IL-17f); II-23; Cx3cr1; ptpn22; TNFa;NOD2/CARD15 for IBD; IL-6; IL-12 (IL-12a; IL-12b): CTLA4; Cx3cl1Parkinson's Disease x-Synuclein; DJ-1; LRRK2; Parkin; PINK1

TABLE B Blood and Anemia (CDAN1, CDA1, RPS19, DBA, PKLR, PK1, NT5C3,UMPH1, coagulation diseases PSN1, RHAG, RH50A, NRAMP2, SPTB, ALAS2,ANH1, ASB, and disorders ABCB7, ABC7, ASAT); Bare lymphocyte syndrome(TAPBP, TPSN, TAP2, ABCB3, PSF2, RING11, MHC2TA, C2TA, RFX5, RFXAP,RFX5), Bleeding disorders (TBXA2R, P2RX1, P2X1); Factor H and factorH-like 1 (HF1, CFH, HUS); Factor V and factor VIII (MCFD2); Factor VIIdeficiency (F7); Factor X deficiency (F10); Factor XI deficiency (F11);Factor XII deficiency (F12, HAF); Factor XIIIA deficiency (F13A1, F13A);Factor XIIIB deficiency (F13B); Fanconi anemia (FANCA, FACA, FA1, FA,FAA, FAAP95, FAAP90, FLJ34064, FANCB, FANCC, FACC, BRCA2, FANCD1,FANCD2, FANCD, FACD, FAD, FANCE, FACE, FANCF, XRCC9, FANCG, BRIP1,BACH1, FANCJ, PHF9, FANCL, FANCM, KIAA1596); Hemophagocyticlymphohistiocytosis disorders (PRF1, HPLH2, UNC13D, MUNC13-4, HPLH3,HLH3, FHL3); Hemophilia A (F8, F8C, HEMA); Hemophilia B (F9, HEMB),Hemorrhagic disorders (PI, ATT, F5); Leukocyde deficiencies anddisorders (ITGB2, CD18, LCAMB, LAD, EIF2B1, EIF2BA, EIF2B2, EIF2B3,EIF2B5, LVWM, CACH, CLE, EIF2B4); Sickle cell anemia (HBB); Thalassemia(HBA2, HBB, HBD, LCRB, HBA1). Cell dysregulation B-cell non-Hodgkinlymphoma (BCL7A, BCL7); Leukemia, (TAL1, and oncology TCL5, SCL, TAL2,FLT3, NBS1, NBS, ZNFN1A1, IK1, LYF1, diseases and disorders HOXD4,HOX4B, BCR, CML, PHL, ALL, ARNT, KRAS2, RASK2, GMPS, AF10, ARHGEF12,LARG, KIAA0382, CALM, CLTH, CEBPA, CEBP, CHIC2, BTL, FLT3, KIT, PBT,LPP, NPM1, NUP214, D9S46E, CAN, CAIN, RUNX1, CBFA2, AML1, WHSC1L1, NSD3,FLT3, AF1Q, NPM1, NUMA1, ZNF145, PLZF, PML, MYL, STAT5B, AF10, CALM,CLTH, ARL11, ARLTS1, P2RX7, P2X7, BCR, CML, PHL, ALL, GRAF, NF1, VRNF,WSS, NFNS, PTPN11, PTP2C, SHP2, NS1, BCL2, CCND1, PRAD1, BCL1, TCRA,GATA1, GF1, ERYF1, NFE1, ABL1, NQO1, DIA4, NMOR1, NUP214, D9S46E, CAN,CAIN). Inflammation and AIDS (KIR3DL1, NKAT3, NKB1, AMB11, KIR3DS1,IFNG, CXCL12, immune related SDF1); Autoimmune lymphoproliferativesyndrome (TNFRSF6, APT1, diseases and disorders FAS, CD95, ALPS1A);Combined immunodeficiency, (IL2RG, SCIDX1, SCIDX, IMD4); HIV-1 (CCL5,SCYA5, D17S136E, TCP228), HIV susceptibility or infection (IL10, CSIF,CMKBR2, CCR2, CMKBR5, CCCKR5 (CCR5)); Immunodeficiencies (CD3E, CD3G,AICDA, AID, HIGM2, TNFRSF5, CD40, UNG, DGU, HIGM4, TNFSF5, CD40LG,HIGM1, IGM, FOXP3, IPEX, AIID, XPID, PIDX, TNFRSF14B, TACI);Inflammation (IL-10, IL-1 (IL-1a, IL-1b), IL-13, IL-17 (IL-17a (CTLA8),IL-17b, IL-17c, IL-17d, IL-17F), II-23, Cx3cr1, ptpn22, TNFa,NOD2/CARD15 for IBD, IL-6, IL-12 (IL-12a, IL-12b), CTLA4, Cx3cl1);Severe combined immunodeficiencies (SCIDs)(JAK3, JAKL, DCLRE1C, ARTEMIS,SCIDA, RAG1, RAG2, ADA, PTPRC, CD45, LCA, IL7R, CD3D, T3D, IL2RG,SCIDX1, SCIDX, IMD4). Metabolic, liver, Amyloid neuropathy (TTR, PALB);Amyloidosis (APOA1, APP, AAA, kidney and protein CVAP, AD1, GSN, FGA,LYZ, TTR, PALB); Cirrhosis (KRT18, KRT8, diseases and disorders CIRH1A,NAIC, TEX292, KIAA1988); Cystic fibrosis (CFTR, ABCC7, CF, MRP7);Glycogen storage diseases (SLC2A2, GLUT2, G6PC, G6PT, G6PT1 , GAA,LAMP2, LAMPB, AGL, GDE, GBE1, GYS2, PYGL, PFKM); Hepatic adenoma, 142330(TCF1, HNF1A, MODY3), Hepatic failure, early onset, and neurologicdisorder (SCOD1, SCO1), Hepatic lipase deficiency (LIPC),Hepatoblastoma, cancer and carcinomas (CTNNB1, PDGFRL, PDGRL, PRLTS,AXIN1, AXIN, CTNNB1, TP53, P53, LFS1, IGF2R, MPRI, MET, CASP8, MCH5;Medullary cystic kidney disease (UMOD, HNFJ, FJHN, MCKD2, ADMCKD2);Phenylketonuria (PAH, PKU1, QDPR, DHPR, PTS); Polycystic kidney andhepatic disease (FCYT, PKHD1, ARPKD, PKD1, PKD2, PKD4, PKDTS, PRKCSH,G19P1, PCLD, SEC63). Muscular/Skeletal Becker muscular dystrophy (DMD,BMD, MYF6), Duchenne Muscular diseases and disorders Dystrophy (DMD,BMD); Emery-Dreifuss muscular dystrophy (LMNA, LMN1, EMD2, FPLD, CMD1A,HGPS, LGMD1B, LMNA, LMN1, EMD2, FPLD, CMD1A); Facioscapulohumeralmuscular dystrophy (FSHM1A, FSHD1A); Muscular dystrophy (FKRP, MDC1C,LUMD2I, LAMA2, LAMM, LARGE, KIAA0609, MDC1D, FCMD TTID, MYOT, CAPN3,CANP3, DYSF, LGMD2B, SGCG, LGMD2C, DMDA1, SCG3, SGCA, ADL, DAG2, LGMD2D,DMDA2, SGCB, LGMD2E, SGCD, SGD, LGMD2F, CMD1L, TCAP, LGMD2G, CMD1N,TRIM32, HT2A, LGMD2H, FKRP, MDC1C, LGMD2I, TTN, CMD1G, TMD, LGMD2J,POMT1, CAV3, LGMD1C, SEPN1, SELN, RSMD1, PLEC1, PLTN, EBS1);Osteopetrosis (LRP5, BMND1, LRP7, LR3, OPPG, VBCH2, CLCN7, CLC7, OPTA2,OSTM1, GL, TCIRG1, TIRC7, OC116, OPTB1); Muscular atrophy (VAPB, VAPC,ALS8, SMN1, SMA1, SMA2, SMA3, SMA4, BSCL2, SPG17, GARS, SMAD1, CMT2D,HEXB, IGHMBP2, SMUBP2, CATF1, SMARD1). Neurological and ALS (SOD1, ALS2,STEX, FUS, TARDBP, VEGF (VEGF-a, VEGF-b, neuronal diseases and VEGF-c);Alzheimer disease (APP, AAA, CVAP, AD1, APOE, AD2, disorders PSEN2, AD4,STM2, APBB2, FE65L1, NOS3, PLAU, URK, ACE, DCP1, ACE1, MPO, PACIP1,PAXIP1L, PTIP, A2M, BLMH, BMH, PSEN1, AD3); Autism (Mecp2, BZRAP1,MDGA2, Sema5A, Neurexin 1, GLO1, MECP2, RTT, PPMX, MRX16, MRX79, NLGN3,NLGN4, KIAA1260, AUTSX2); Fragile X Syndrome (FMR2, FXR1, FXR2, mGLUR5);Huntington's disease and disease like disorders (HD, IT15, PRNP, PRIP,JPH3, JP3, HDL2, TBP, SCA17); Parkinson disease (NR4A2, NURR1, NOT,TINUR, SNCAIP, TBP, SCA17, SNCA, NACP, PARK1, PARK4, DJ1, PARK7, LRRK2,PARK8, PINK1, PARK6, UCHL1, PARK5, SNCA, NACP, PARK1, PARK4, PRKN,PARK2, PDJ, DBH, NDUFV2); Rett syndrome (MECP2, RTT, PPMX, MRX16, MRX79,CDKL5, STK9, MECP2, RTT, PPMX, MRX16, MRX79, x-Synuclein, DJ-1);Schizophrenia (Neuregulin1 (Nrg1), Erb4 (receptor for Neuregulin),Complexin1 (Cplx1), Tph1 Tryptophan hydroxylase, Tph2, Tryptophanhydroxylase 2, Neurexin 1, GSK3, GSK3a, GSK3b, 5-HTT (Slc6a4), COMT, DRD(Drd1a), SLC6A3, DAOA, DTNBP1, Dao (Dao1)); Secretase Related Disorders(APH-1 (alpha and beta), Presenilin (Psen1), nicastrin, (Ncstn), PEN-2,Nos1, Parp1, Nat1, Nat2); Trinucleotide Repeat Disorders (HTT(Huntington's Dx), SBMA/SMAX1/AR (Kennedy's Dx), FXN/X25 (Friedrich'sAtaxia), ATX3 (Machado-Joseph's Dx), ATXN1 and ATXN2 (spinocerebellarataxias), DIVITK (myotonic dystrophy), Atrophin-1 and Atn1 (DRPLA Dx),CBP (Crete-BP—global instability), VLDLR (Alzheimer's), Atxn7, Atxn10).Occular diseases and Age-related macular degeneration (Abcr, Ccl2, Cc2,cp ceruloplasmin), disorders Timp3, cathepsinD, Vldlr, Ccr2); Cataract(CRYAA, CRYA1, CRYBB2, CRYB2, PITX3, BFSP2, CP49, CP47, CRYAA, CRYA1,PAX6, AN2, MGDA, CRYBA1, CRYB1, CRYGC, CRYG3, CCL, LIM2, MP19, CRYGD,CRYG4, BFSP2, CP49, CP47, HSF4, CTM, HSF4, CTM, MIP, AQP0, CRYAB, CRYA2,CTPP2, CRYBB1, CRYGD, CRYG4, CRYBB2, CRYB2, CRYGC, CRYG3, CCL, CRYAA,CRYA1, GJA8, CX50, CAE1, GJA3, CX46, CZP3, CAE3, CCM1, CAM, KRIT1);Corneal clouding and dystrophy (APOA1, TGFBI, CSD2, CDGG1, CSD, BIGH3,CDG2, TACSTD2, TROP2, M1S1, VSX1, RINX, PPCD PPD, KTCN, COL8A2, FECD,PPCD2, PIP5K3, CFD); Cornea plana congenital (KERA, CNA2); Glaucoma(MYOC, TIGR, GLC1A, JOAG, GPOA, OPTN, GLC1E, FIP2, HYPL, NRP, CYP1B1,GLC3A, OPA1, NTG, NPG, CYP1B1, GLC3A); Leber congenital amaurosis (CRB1,RP12, CRX, CORD2, CRD, RPGRIP1, LCA6, CORD9, RPE65, RP20, AIPL1, LCA4,GUCY2D, GUC2D, LCA1, CORD6, RDH12, LCA3); Macular dystrophy (ELOVL4,ADMD, STGD2, STGD3, RDS, RP7, PRPH2, PRPH, AVMD, AOFMD, VMD2).

TABLE C CELLULAR FUNCTION GENES PI3K/AKT Signaling PRKCE; ITGAM; ITGA5;IRAK1; PRKAA2; EIF2AK2; PTEN; EIF4E; PRKCZ; GRK6; MAPK1; TSC1; PLK1;AKT2; IKBKB; PIK3CA; CDK8; CDKN1B; NFKB2; BCL2; PIK3CB; PPP2R1A; MAPK8;BCL2L1; MAPK3; TSC2; ITGA1; KRAS; EIF4EBP1; RELA; PRKCD; NOS3; PRKAA1;MAPK9; CDK2; PPP2CA; PIM1; ITGB7; YWHAZ; ILK; TP53; RAF1; IKBKG; RELB;DYRK1A; CDKN1A; ITGB1; MAP2K2; JAK1; AKT1; JAK2; PIK3R1; CHUK; PDPK1;PPP2R5C; CTNNB1; MAP2K1; NFKB1; PAK3; ITGB3; CCND1; GSK3A; FRAP1; SFN;ITGA2; TTK; CSNK1A1; BRAF; GSK3B; AKT3; FOXO1; SGK; HSP90AA1; RPS6KB1ERK/MAPK Signaling PRKCE; ITGAM; ITGA5; HSPB1; IRAK1; PRKAA2; EIF2AK2;RAC1; RAP1A; TLN1; EIF4E; ELK1; GRK6; MAPK1; RAC2; PLK1; AKT2; PIK3CA;CDK8; CREB1; PRKCI; PTK2; FOS; RPS6KA4; PIK3CB; PPP2R1A; PIK3C3; MAPK8;MAPK3; ITGA1; ETS1; KRAS; MYCN; EIF4EBP1; PPARG; PRKCD; PRKAA1; MAPK9;SRC; CDK2; PPP2CA; PIM1; PIK3C2A; ITGB7; YWHAZ; PPP1CC; KSR1; PXN; RAF1;FYN; DYRK1A; ITGB1; MAP2K2; PAK4; PIK3R1; STAT3; PPP2R5C; MAP2K1; PAK3;ITGB3; ESR1; ITGA2; MYC; TTK; CSNK1A1; CRKL; BRAF; ATF4; PRKCA; SRF;STAT1; SGK Glucocorticoid Receptor RAC1; TAF4B; EP300; SMAD2; TRAF6;PCAF; ELK1; Signaling MAPK1; SMAD3; AKT2; IKBKB; NCOR2; UBE2I; PIK3CA;CREB1; FOS; HSPA5; NFKB2; BCL2; MAP3K14; STAT5B; PIK3CB; PIK3C3; MAPK8;BCL2L1; MAPK3; TSC22D3; MAPK10; NRIP1; KRAS; MAPK13; RELA; STAT5A;MAPK9; NOS2A; PBX1; NR3C1; PIK3C2A; CDKN1C; TRAF2; SERPINE1; NCOA3;MAPK14; TNF; RAF1; IKBKG; MAP3K7; CREBBP; CDKN1A; MAP2K2; JAK1; IL8;NCOA2; AKT1; JAK2; PIK3R1; CHUK; STAT3; MAP2K1; NFKB1; TGFBR1; ESR1;SMAD4; CEBPB; JUN; AR; AKT3; CCL2; MMP1; STAT1; IL6; HSP90AA1 AxonalGuidance PRKCE; ITGAM; ROCK1; ITGA5; CXCR4; ADAM12; Signaling IGF1;RAC1; RAP1A; EIF4E; PRKCZ; NRP1; NTRK2; ARHGEF7; SMO; ROCK2; MAPK1; PGF;RAC2; PTPN11; GNAS; AKT2; PIK3CA; ERBB2; PRKCI; PTK2; CFL1; GNAQ;PIK3CB; CXCL12; PIK3C3; WNT11; PRKD1; GNB2L1; ABL1; MAPK3; ITGA1; KRAS;RHOA; PRKCD; PIK3C2A; ITGB7; GLI2; PXN; VASP; RAF1; FYN; ITGB1; MAP2K2;PAK4; ADAM17; AKT1; PIK3R1; GLI1; WNT5A; ADAM10; MAP2K1; PAK3; ITGB3;CDC42; VEGFA; ITGA2; EPHA8; CRKL; RND1; GSK3B; AKT3; PRKCA EphrinReceptor PRKCE; ITGAM; ROCK1; ITGA5; CXCR4; IRAK1; Signaling PRKAA2;EIF2AK2; RAC1 ; RAP1A; GRK6; ROCK2; MAPK1; PGF; RAC2; PTPN11; GNAS;PLK1; AKT2; DOK1; CDK8; CREB1; PTK2; CFL1; GNAQ; MAP3K14; CXCL12; MAPK8;GNB2L1; ABL1; MAPK3; ITGA1; KRAS; RHOA; PRKCD; PRKAA1; MAPK9; SRC; CDK2;PIM1; ITGB7; PXN; RAF1; FYN; DYRK1A; ITGB1; MAP2K2; PAK4; AKT1; JAK2;STAT3; ADAM10; MAP2K1; PAK3; ITGB3; CDC42; VEGFA; ITGA2; EPHA8; TTK;CSNK1A1; CRKL; BRAF; PTPN13; A1F4; AKT3; SGK Actin Cytoskeleton ACTN4;PRKCE; ITGAM; ROCK1; ITGA5; IRAK1; Signaling PRKAA2; EIF2AK2; RAC1; INS;ARHGEF7; GRK6; ROCK2; MAPK1; RAC2; PLK1; AKT2; PIK3CA; CDK8; PTK2; CFL1;PIK3CB; MYH9; DIAPH1; PIK3C3; MAPK8; F2R; MAPK3; SLC9A1; ITGA1; KRAS;RHOA; PRKCD; PRKAA1; MAPK9; CDK2; PIM1; PIK3C2A; ITGB7; PPP1CC; PXN;VIL2; RAF1; GSN; DYRK1A; ITGB1 MAP2K2; PAK4; PIP5K1A; PIK3R1; MAP2K1;PAK3; ITGB3; CDC42; APC; ITGA2; TTK; CSNK1A1; CRKL; BRAF; VAV3; SGKHuntington's Disease PRKCE; IGF1; EP300; RCOR1; PRKCZ; HDAC4; TGM2;Signaling MAPK1; CAPNS1; AKT2; EGFR; NCOR2; SP1; CAPN2; PIK3CA; HDAC5;CREB1; PRKCI; HSPA5; REST; GNAQ; PIK3CB; PIK3C3; MAPK8; IGF1R; PRKD1;GNB2L1; BCL2L1; CAPN1; MAPK3; CASP8; HDAC2; HDAC7A; PRKCD; HDAC11;MAPK9; HDAC9; PIK3C2A; HDAC3; TP53; CASP9; CREBBP; AKT1; PIK3R1; PDPK1;CASP1; APAF1; FRAP1; CASP2; JUN; BAX; ATF4; AKT3; PRKCA; CLTC; SGK;HDAC6; CASP3 Apoptosis Signaling PRKCE; ROCK1; BID; IRAK1; PRKAA2;EIF2AK2; BAK1; BIRC4; GRK6; MAPK1; CAPNS1; PLK1; AKT2; IKBKB; CAPN2;CDK8; FAS; NFKB2; BCL2; MAP3K14; MAPK8; BCL2L1; CAPN1; MAPK3; CASP8;KRAS; RELA; PRKCD; PRKAA1; MAPK9; CDK2; PIM1; TP53; TNF; RAF1; IKBKG;RFLB; CASP9; DYRK1A; MAP2K2; CHUK; APAF1; MAP2K1; NFKB1; PAK3; LMNA;CASP2; BIRC2; TTK; CSNK1A1; BRAF; BAX; PRKCA; SGK; CASP3; BIRC3; PARP1 BCell Receptor RAC1; PTEN; LYN; ELK1; MAPK1; RAC2; PTPN11; SignalingAKT2; IKBKB; PIK3CA; CREB1; SYK; NFKB2; CAMK2A; MAP3K14; PIK3CB; PIK3C3;MAPK8; BCL2L1; ABL1; MAPK3; ETS1; KRAS; MAPK13; RELA; PTPN6; MAPK9;EGR1; PIK3C2A; BTK; MAPK14; RAF1; IKBKG; RELB; MAP3K7; MAP2K2; AKT1;PIK3R1; CHUK; MAP2K1; NFKB1; CDC42; GSK3A; FRAP1; BCL6; BCL10; JUN;GSK3B; ATF4; AKT3; VAV3; RPS6KB1 Leukocyte Extravasation ACTN4; CD44;PRKCE; ITGAM; ROCK1; CXCR4; CYBA; Signaling RAC1; RAP1A; PRKCZ; ROCK2;RAC2; PTPN11; MMP14; PIK3CA; PRKCI; PTK2; PIK3CB; CXCL12; PIK3C3; MAPK8;PRKD1; ABL1; MAPK10; CYBB; MAPK13; RHOA; PRKCD; MAPK9; SRC; PIK3C2A;BTK; MAPK14; NOX1; PXN; VIL2; VASP; ITGB1; MAP2K2; CTNND1; PIK3R1;CTNNB1; CLDN1; CDC42; F11R; ITK; CRKL; VAV3; CTTN; PRKCA; MMP1; MMP9Integrin Signaling ACTN4; ITGAM; ROCK1; ITGA5; RAC1; PTEN; RAP1A; TLN1;ARHGEF7; MAPK1; RAC2; CAPNS1; AKT2; CAPN2; PIK3CA; PTK2; PIK3CB; PIK3C3;MAPK8; CAV1; CAPN1; ABL1; MAPK3; ITGA1; KRAS; RHOA; SRC; PIK3C2A; ITGB7;PPP1CC; ILK; PXN; VASP; RAF1; FYN; ITGB1; MAP2K2; PAK4; AKT1; PIK3R1;TNK2; MAP2K1; PAK3; ITGB3; CDC42; RND3; ITGA2; CRKL; BRAF; GSK3B; AKT3Acute Phase Response IRAK1; SOD2; MYD88; TRAF6; ELK1; MAPK1; PTPN11;Signaling AKT2; IKBKB; PIK3CA; FOS; NFKB2; MAP3K14; PIK3CB; MAPK8;RIPK1; MAPK3; IL6ST; KRAS; MAPK13; IL6R; RELA; SOCS1; MAPK9; FTL; NR3C1;TRAF2; SERPINE1; MAPK14; TNF; RAF1; PDK1; IKBKG; RELB; MAP3K7; MAP2K2;AKT1; JAK2; PIK3R1; CHUK; STAT3; MAP2K1; NFKB1; FRAP1; CEBPB; JUN; AKT3;IL1R1; IL6 PTEN Signaling ITGAM; ITGA5; RAC1; PTEN; PRKCZ; BCL2L11;MAPK1; RAC2; AKT2; EGFR; IKBKB; CBL; PIK3CA; CDKN1B; PTK2; NFKB2; BCL2;PIK3CB; BCL2L1; MAPK3; ITGA1; KRAS; ITGB7; ILK; PDGFRB; INSR; RAF1;IKBKG; CASP9; CDKN1A; ITGB1; MAP2K2; AKT1; PIK3R1; CHUK; PDGFRA; PDPK1;MAP2K1; NFKB1; ITGB3; CDC42; CCND1; GSK3A; ITGA2; GSK3B; AKT3; FOXO1;CASP3; RPS6KB1 p53 Signaling PTEN; EP300; BBC3; PCAF; FASN; BRCA1;GADD45A; BIRC5; AKT2; PIK3CA; CHEK1; TP53INP1; BCL2; PIK3CB; PIK3C3;MAPK8; THBS1; ATR; BCL2L1; E2F1; PMAIP1; CHEK2; TNFRSF10B; TP73; RB1;HDAC9; CDK2; PIK3C2A; MAPK14; TP53; LRDD; CDKN1A; HIPK2; AKT1; PIK3R1;RRM2B; APAF1; CTNNB1; SIRT1; CCND1; PRKDC; ATM; SFN; CDKN2A; JUN; SNAI2;GSK3B; BAX; AKT3 Aryl Hydrocarbon HSPB1; EP300; FASN; TGM2; RXRA; MAPK1;NQO1; Receptor Signaling NCOR2; SP1; ARNT; CDKN1B; FOS; CHEK1; SMARCA4;NFKB2; MAPK8; ALDH1A1; ATR; E2F1; MAPK3; NRIP1; CHEK2; RELA; TP73;GSTP1; RB1; SRC; CDK2; AHR; NFE2L2; NCOA3; TP53; TNF; CDKN1A; NCOA2;APAF1; NFKB1; CCND1; ATM; ESR1; CDKN2A; MYC; JUN; ESR2; BAX; IL6;CYP1B1; HSP90AA1 Xenobiotic Metabolism PRKCE; EP300; PRKCZ; RXRA; MAPK1;NQO1; Signaling NCOR2; PIK3CA; ARNT; PRKCI; NFKB2; CAMK2A; PIK3CB;PPP2R1A; PIK3C3; MAPK8; PRKD1; ALDH1A1; MAPK3; NRIP1; KRAS; MAPK13;PRKCD; GSTP1; MAPK9; NOS2A; ABCB1; AHR; PPP2CA; FTL; NFE2L2; PIK3C2A;PPARGC1A; MAPK14; TNF; RAF1; CREBBP; MAP2K2; PIK3R1; PPP2R5C; MAP2K1;NFKB1; KEAP1; PRKCA; EIF2AK3; IL6; CYP1B1; HSP90AA1 SAPK/JNK SignalingPRKCE; IRAK1; PRKAA2; EIF2AK2; RAC1; ELK1; GRK6; MAPK1; GADD45A; RAC2;PLK1; AKT2; PIK3CA; FADD; CDK8; PIK3CB; PIK3C3; MAPK8; RIPK1; GNB2L1 ;IRS1; MAPK3; MAPK10; DAXX; KRAS; PRKCD; PRKAA1; MAPK9; CDK2; PIM1;PIK3C2A; TRAF2; TP53; LCK; MAP3K7; DYRK1A; MAP2K2; PIK3R1; MAP2K1; PAK3;CDC42; JUN; TTK; CSNK1A1 ; CRKL; BRAF; SGK PPAr/RXR Signaling PRKAA2;EP300; INS; SMAD2; TRAF6; PPARA; FASN; RXRA; MAPK1; SMAD3; GNAS; IKBKB;NCOR2; ABCA1; GNAQ; NFKB2; MAP3K14; STAT5B; MAPK8; IRS1; MAPK3; KRAS;RELA; PRKAA1; PPARGC1A; NCOA3; MAPK14; INSR; RAF1; IKBKG; RELB; MAP3K7;CREBBP; MAP2K2; JAK2; CHUK; MAP2K1; NFKB1; TGFBR1; SMAD4; JUN; IL1R1;PRKCA; IL6; HSP90AA1; ADIPOQ NF-KB Signaling IRAK1; EIF2AK2; EP300; INS;MYD88; PRKCZ; TRAF6; TBK1; AKT2; EGFR; IKBKB; PIK3CA; BTRC; NFKB2;MAP3K14; PIK3CB; PIK3C3; MAPK8; RIPK1; HDAC2; KRAS; RELA; PIK3C2A;TRAF2; TLR4; PDGRB; TNF; INSR; LCK; IKBKG; RELB; MAP3K7; CREBBP; AKT1;PIK3R1; CHUK; PDGFRA; NFKB1; TLR2; BCL10; GSK3B; AKT3; TNFAIP3; IL1R1Neuregulin Signaling ERBB4; PRKCE; ITGAM; ITGA5; PTEN; PRKCZ; ELK1;MAPK1; PTPN11; AKT2; EGFR; ERBB2; PRKCI; CDKN1B; STAT5B; PRKD1; MAPK3;ITGA1; KRAS; PRKCD, STAT5A, SRC; ITGB7; RAF1; ITGB1; MAP2K2; ADAM17;AKT1; PIK3R1; PDPK1; MAP2K1; ITGB3; EREG; FRAP1; PSEN1; ITGA2; MYC;NRG1; CRKL; AKT3; PRKCA; HSP90AA1; RPS6KB1 Wnt & Beta catenin CD44;EP300; LRP6; DVL3; CSNK1E; GJA1; SMO; Signaling AKT2, PIN1; CDH1; BTRC;GNAQ; MARK2; PPP2R1A WNT11; SRC; DKK1; PPP2CA; SOX6; SFRP2; ILK; LEF1;SOX9; TP53; MAP3K7; CREBBP; TCF7L2; AKT1 PPP2R5C; WNT5A; LRP5; CTNNB1;TGFBR1; CCND1; GSK3A; DVL1; APC; CDKN2A; MYC; CSNK1A1; GSK3B AKT3; SOX2Insulin Receptor PTEN; INS; EIF4E; PTPN1; PRKCZ; MAPK1; TSC1; SignalingPTPN11; AKT2; CBL; PIK3CA; PRKCI; PIK3CB; PIK3C3; MAPK8; IRS1; MAPK3;TSC2; KRAS; EIF4EBP1; SLC2A4; PIK3C2A; PPP1CC; INSR; RAF1; MAP2K1;GSK3A; FRAP1; CRKL; GSK3B; AKT3; FOXO1; SGK; RPS6KB1 IL-6 SignalingHSPB1; TRAF6; MAPKAPK2; ELK1; MAPK1; PTPN11; IKBKB; FOS; NFKB2; MAP3K14;MAPK8; MAPK3; MAPK10; IL6ST; KRAS; MAPK13; IL6R; RELA; SOCS1; MAPK9;ABCB1; TRAF2; MAPK14; TNF; RAF1; IKBKG; RELB; MAP3K7; MAP2K2; IL8; JAK2;CHUK; STAT3; MAP2K1; NFKB1; CEBPB; JUN; IL1R1; SRF; IL6 HepaticCholestasis PRKCE; IRAK1; INS; MYD88; PRKCZ; TRAF6; PPARA; RXRA; IKBKB;PRKCI; NFKB2; MAP3K14; MAPK8; PRKD1; MAPK10; RELA; PRKCD; MAPK9; ABCB1;TRAF2; TLR4; TNF; INSR; IKBKG; RELB; MAP3K7; IL8; CHUK; NR1H2; TJP2;NFKB1; ESR1; SREBF1; FGFR4; JUN; IL1R1; PRKCA; IL6 IGF-1 Signaling IGF1;PRKCZ; ELK1; MAPK1; PTPN11; NEDD4; AKT2; PIK3CA; PRKCI; PTK2; FOS;PIK3CB; PIK3C3; MAPK8; IGF1R; IRS1; MAPK3; IGFBP7; FRAS; PIK3C2A; YWHAZ;PXN; RAF1; CASP9; MAP2K2; AKT1; PIK3R1; PDPK1; MAP2K1; IGFBP2; SFN; JUN;CYR61; AKT3; FOXO1; SRF; CTGF; RPS6KB1 NRF2-mediated PRKCE; EP300; SOD2;PRKCZ; MAPK1; SQSTM1; Oxidative NQO1; PIK3CA; PRKCI; FOS; PIK3CB;PIK3C3; MAPK8; Stress Response PRKD1; MAPK3; KRAS; PRKCD; GSTP1; MAPK9;FTL; NFE2L2; PIK3C2A; MAPK14; RAF1; MAP3K7; CREBBP; MAP2K2; AKT1;PIK3R1; MAP2K1; PPIB; JUN; KEAP1; GSK3B; ATF4; PRKCA; EIF2AK3; HSP90AA1Hepatic Fibrosis/Hepatic EDN1; IGF1; KDR; FLT1; SMAD2; FGFR1; MET; PGF;Stellate Cell Activation SMAD3; EGFR; FAS; CSF1; NFKB2; BCL2; MYH9;IGF1R; IL6R; RELA; TLR4; PDGFRB; TNF; RELB; IL8; PDGFRA; NFKB1; TGFBR1;SMAD4; VEGFA; BAX; IL1R1; CCL2; HGF; MMP1; STAT1; IL6; CTGF; MMP9 PPARSignaling EP300; INS; TRAF6; PPARA; RXRA; MAPK1; IKBKB; NCOR2; FOS;NFKB2; MAP3K14; STAT5B; MAPK3; NRIP1; KRAS; PPARG; RELA; STAT5A; TRAF2;PPARGC1A; PDGFRB; TNF; INSR; RAF1; IKBKG; RELB; MAP3K7; CREBBP; MAP2K2;CHUK; PDGFRA; MAP2K1; NFKB1; JUN; IL1R1; HSP90AA1 Fc Epsilon RISignaling PRKCE; RAC1; PRKCZ; LYN; MAPK1; RAC2; PTPN11; AKT2; PIK3CA;SYK; PRKCI; PIK3CB; PIK3C3; MAPK8; PRKD1; MAPK3; MAPK10; KRAS; MAPK13;PRKCD; MAPK9; PIK3C2A; BTK; MAPK14; TNF; RAF1; FYN; MAP2K2; AKT1;PIK3R1; PDPK1; MAP2K1; AKT3; VAV3; PRKCA G-Protein Coupled PRKCE; RAP1A;RGS16; MAPK1; GNAS; AKT2; IKBKB; Receptor Signaling PIK3CA; CREB1; GNAQ;NFKB2; CAMK2A; PIK3CB; PIK3C3: MAPK3; KRAS; RELA; SRC; PIK3C2A; RAF1;IKBKG; RELB; FYN; MAP2K2; AKT1; PIK3R1; CHUK; PDPK1; STAT3; MAP2K1;NFKB1; BRAF; ATF4; AKT3; PRKCA Inositol Phosphate PRKCE; IRAK1; PRKAA2;EIF2AK2; PTEN; GRK6; Metabolism MAPK1; PLK1; AKT2; PIK3CA; CDK8; PIK3CB;PIK3C3; MAPK8; MAPK3; PRKCD; PRKAA1; MAPK9; CDK2; PIM1; PIK3C2A; DYRK1A;MAP2K2; PIP5K1A; PIK3R1; MAP2K1; PAK3; ATM; TTK; CSNK1A1; BRAF; SGK PDGFSignaling EIF2AK2; ELK1; ABL2; MAPK1; PIK3CA; FOS; PIK3CB; PIK3C3;MAPK8; CAV1; ABL1; MAPK3; KRAS; SRC; PIK3C2A; PDGFRB; RAF1; MAP2K2;JAK1; JAK2; PIK3R1; PDGFRA; STAT3; SPHK1; MAP2K1; MYC; JUN; CRKL; PRKCA;SRF; STAT1; SPHK2 VEGF Signaling ACTN4; ROCK1; KDR; FLT1; ROCK2; MAPK1;PGF; AKT2; PIK3CA; ARNT; PTK2; BCL2; PIK3CB; PIK3C3; BCL2L1; MAPK3;KRAS; HIF1A; NOS3; PIK3C2A; PXN; RAF1; MAP2K2; ELAVL1; AKT1; PIK3R1;MAP2K1; SFN; VEGFA; AKT3; FOXO1; PRKCA Natural Killer Cell PRKCE; RAC1;PRKCZ; MAPK1; RAC2; PTPN11; Signaling KIR2DL3; AKT2; PIK3CA; SYK; PRKCI;PIK3CB; PIK3C3; PRKD1; MAPK3; KRAS; PRKCD; PTPN6; PIK3C2A; LCK; RAF1;FYN; MAP2K2; PAK4; AKT1; PIK3R1; MAP2K1; PAK3; AKT3; VAV3; PRKCA CellCycle: Gl/S HDAC4; SMAD3; SUV39H1; HDAC5; CDKN1B; BTRC; CheckpointRegulation ATR; ABL1; E2F1; HDAC2; HDAC7A; RB1; HDAC11; HDAC9; CDK2;E2F2; HDAC3; TP53; CDKN1A; CCND1; E2F4; ATM; RBL2; SMAD4; CDKN2A; MYC;NRG1; GSK3B; RBL1; HDAC6 T Cell Receptor RAC1; ELK1; MAPK1; IKBKB; CBL;PIK3CA; FOS; Signaling NFKB2; PIK3GB; PIK3C3; MAPK8; MAPK3; KRAS; RELA;PIK3C2A; BTK; LCK; RAF1; IKBKG; RELB; FYN; MAP2K2; PIK3R1; CHUK; MAP2K1;NFKBI; ITK; BCL10; JUN; VAV3 Death Receptor Signaling CRADD; HSPB1; BID;BIRC4; TBK1; IKBKB; FADD; FAS; NFKB2; BCL2; MAP3K14; MAPK8; RIPK1;CASP8; DAXX; TNFRSF10B; RELA; TRAF2; TNF; IKBKG; RELB; CASP9; CHUK;APAF1; NFKB1; CASP2; BIRC2; CASP3; BIRC3 FGF Signaling RAC1; FGFR1; MET;MAPKAPK2; MAPK1; PTPN11; AKT2; PIK3CA; CREB1; PIK3CB; PIK3C3; MAPK8;MAPK3; MAPK13; PTPN6; PIK3C2A; MAPK14; RAF1; AKT1; PIK3R1; STAT3;MAP2K1; FGFR4; CRKL; ATF4; AKT3; PRKCA; HGF GM-CSF Signaling LYN; ELK1;MAPK1; PTPN11; AKT2; PIK3CA; CAMK2A; STAT5B; PIK3CB; PIK3C3; GNB2L1;BCL2L1; MAPK3; ETS1; KRAS; RUNX1; PIM1; PIK3C2A; RAF1; MAP2K2; AKT1;JAK2; PIK3R1; STAT3; MAP2K1; CCND1; AKT3; STAT1 Amyotrophic Lateral BID;IGF1; RAC1; BIRC4; PGF; CAPNS1; CAPN2; Sclerosis Signaling PIK3CA; BCL2;PIK3CB; PIK3C3; BCL2L1; CAPN1; PIK3C2A; TP53; CASP9; PIK3R1; RAB5A;CASP1; APAF1; VEGFA; BIRC2; BAX; AKT3; CASP3; BIRC3 JAK/Stat SignalingPTPN1; MAPK1; PTPN11; AKT2; PIK3CA; STAT5B; PIK3CB; PIK3C3; MAPK3; KRAS;SOCS1; STAT5A; PTPN6; PIK3C2A; RAF1; CDKN1A; MAP2K2; JAK1; AKT1; JAK2;PIK3R1; STAT3; MAP2K1; FRAP1; AKT3; STAT1 Nicotinate and PRKCE; IRAK1;PRKAA2; EIF2AK2; GRK6; MAPK1; Nicotinamide PLK1; AKT2; CDK8; MAPK8;MAPK3; PRKCD; PRKAA1; Metabolism PBEF1; MAPK9; CDK2; PIM1; DYRK1A;MAP2K2; MAP2K1; PAK3; NT5E; TTK; CSNK1A1; BRAF; SGK Chemokine SignalingCXCR4; ROCK2; MAPK1; PTK2; FOS; CFL1; GNAQ; CAMK2A; CXCL12; MAPK8;MAPK3; KRAS; MAPK13; RHOA; CCR3; SRC; PPP1CC; MAPK14; NOX1; RAF1;MAP2K2; MAP2K1; JUN; CCL2; PRKCA IL-2 Signaling ELK1; MAPK1; PTPN11;AKT2; PIK3CA; SYK; FOS; STAT5B; PIK3CB; PIK3C3; MAPK8; MAPK3; KRAS;SOCS1; STAT5A; PIK3C2A; LCK; RAF1; MAP2K2; JAK1; AKT1; PIK3R1; MAP2K1;JUN; AKT3 Synaptic Long Term PRKCE; IGF1; PRKCZ; PRDX6; LYN; MAPK1;GNAS; Depression PRKCI; GNAQ; PPP2R1A; IGF1R; PRKD1; MAPK3; KRAS; GRN;PRKCD; NOS3; NOS2A; PPP2CA; YWHAZ; RAF1; MAP2K2; PPP2R5C; MAP2K1; PRKCAEstrogen Receptor TAF4B; EP300; CARM1; PCAF; MAPK1; NCOR2; SignalingSMARCA4; MAPK3; NRIP1; KRAS; SRC; NR3C1; HDAC3; PPARGC1A; RBM9; NCOA3;RAF1; CREBBP; MAP2K2; NCOA2; MAP2K1; PRKDC; ESR1; ESR2 ProteinUbiquitination TRAF6; SMURF1; BIRC4; BRCA1; UCHL1; NEDD4; Pathway CBL;UBE21; BTRC; HSPA5; USP7; USP10; FBXW7; USP9X; STUB1; USP22; B2M; BIRC2;PARK2; USP8; USP1; VHL; HSP90AA1; BIRC3 IL-10 Signaling TRAF6; CCR1;ELK1; IKBKB; SP1; FOS; NFKB2; MAP3K14; MAPK8; MAPK13; RELA; MAPK14; TNF;IKBKG; RELB; MAP3K7; JAK1; CHUK; STAT3; NFKB1; JUN; IL1R1; IL6 VDR/RXRActivation PRKCE; EP300; PRKCZ; RXRA; GADD45A; HES1; NCOR2; SP1; PRKCI;CDKN1B; PRKD1, PRKCD; RUNX2; KLF4; YY1; NCOA3; CDKN1A; NCOA2; SPP1;LRP5; CEBPB; FOXO1; PRKCA TGF-beta Signaling EP300; SMAD2; SMURE1;MAPK1; SMAD3; SMAD1; FOS; MAPK8; MAPK3; KRAS; MAPK9; RUNX2; SERPINE1;RAF1; MAP3K7; CREBBP; MAP2K2; MAP2K1; TGFBRI; SMAD4; JUN; SMAD5Toll-like Receptor IRAK1; EIF2AK2; MYD88; TRAF6; PPARA; ELK1; SignalingIKBKB; FOS; NFKB2; MAP3K14; MAPK8; MAPK13; RELA; TLR4; MAPK14; IKBKG;RELB; MAP3K7; CHUK; NFKB1; TLR2; JUN p38 MAPK Signaling HSPB1; IRAK1;TRAF6; MAPKAPK2; ELK1; FADD; FAS; CREB1; DDIT3; RPS6KA4; DAXX; MAPK13;TRAF2; MAPK14; TNF; MAP3K7; TGFBR1; MYC; ATF4; IL1R1; SRF; STAT1Neurotrophin/TRK NTRK2; MAPK1; PTPN11; PIK3CA; CREB1; FOS; SignalingPIK3CB; PIK3C3; MAPK8; MAPK3; KRAS; PIK3C2A; RAF1; MAP2K2; AKT1; PIK3R1;PDPK1; MAP2K1; CDC42; JUN; ATF4 FXR/RXR Activation INS; PPARA; FASN;RXRA; AKT2; SDC1; MAPK8; APOB; MAPK10; PPARG; MTTP; MAPK9; PPARGC1A;TNF; CREBBP; AKT1; SREBF1; FGFR4; AKT3; FOXO1 Synaptic Long Term PRKCE;RAP1A; EP300; PRKCZ; MAPK1; CREB1; Potentiation PRKCI; GNAQ; CAMK2A;PRKD1; MAPK3; KRAS; PRKCD; PPP1CC; RAF1; CREBBP; MAP2K2; MAP2K1; ATF4;PRKCA Calcium Signaling RAP1A; EP300; HDAC4; MAPK1; HDAC5; CREB1;CAMK2A; MYH9; MAPK3; HDAC2; HDAC7A; HDAC11; HDAC9; HDAC3; CREBBP; CALR;CAMKK2; ATF4; HDAC6 EGF Signaling ELK1; MAPK1; EGFR; PIK3CA; FOS;PIK3CB; PIK3C3; MAPK8; MAPK3; PIK3C2A; RAF1; JAK1; PIK3R1; STAT3;MAP2K1; JUN; PRKCA; SRF; STAT1 Hypoxia Signaling in the EDN1; PTEN;EP300; NQO1; UBE2I; CREB1; ARNT; Cardiovascular System HIF1A; SLC2A4;NOS3; TP53; LDHA; AKTI ; ATM; VEGFA; JUN; ATF4; VHL; HSP90AA1 LPS/IL-1Mediated IRAK1; MYD88; TRAF6; PPARA; RXRA; ABCA1; Inhibition of RXRMAPK8; ALDH1A1; GSTP1; MAPK9; ABCB1; TRAF2; Function TLR4; TNF; MAP3K7;NR1H2; SREBF1; JUN; IL1R1 LXRIRXR Activation FASN; RXRA; NCOR2; ABCA1;NFKB2; IRF3; RELA; NOS2A; TLR4; TNF; RELB; LDLR; NR1H2; NFKB1; SREBF1;IL1R1; CCL2; IL6; MMP9 Amyloid Processing PRKCE; CSNK1E; MAPK1; CAPNS1;AKT2; CAPN2; CAPN1; MAPK3; MAPK13; MAPT; MAPK14; AKT1; PSEN1; CSNK1A1;GSK3B; AKT3; APP IL-4 Signaling AKT2; PIK3CA; PIK3CB; PIK3C3; IRS1;KRAS; SOCS1; PTPN6; NR3C1; PIK3C2A; JAK1; AKT1; JAK2; PIK3R1; FRAP1;AKT3; RPS6KB1 Cell Cycle: G2/M DNA EP300; PCAF; BRCA1; GADD45A; PLK1;BTRC; Damage Checkpoint CHEK1; ATR; CHEK2; YWHAZ; TP53; CDKN1A;Regulation PRKDC; ATM; SFN; CDKN2A Nitric Oxide Signaling KDR; FLT1;PGF; AKT2; PIK3CA; PIK3CB; PIK3C3; in the Cardiovascular CAV1; PRKCD;NOS3; PIK3C2A; AKT1; PIK3R1; System VEGFA; AKT3; HSP90AA1 PurineMetabolism NME2; SMARCA4; MYH9; RRM2; ADAR; EIF2AK4; PKM2; ENTPD1;RAD51; RRM2B; TJP2; RAD51C; NT5E; POLD1; NME1 cAMP-Mediated RAP1A;MAPK1; GNAS; CREB1; CAMK2A; MAPK3; Signaling SRC; RAF1; MAP2K2; STAT3;MAP2K1; BRAF; ATF4 Mitochondrial SOD2; MAPK8; CASP8; MAPK10; MAPK9;CASP9; Dysfunction PARK7; PSEN1; PARK2; APP; CASP3 Notch Signaling HES1;JAG1; NUMB; NOTCH4; ADAM17; NOTCH2; PSEN1; NOTCH3; NOTCH1; DLL4Endoplasmic Reticulum HSPA5; MAPK8; XBP1; TRAF2; ATF6; CASP9; ATF4;Stress Pathway EIF2AK3; CASP3 Pyrimidine Metabolism NME2; AICDA; RRM2;EIF2AK4; ENTPD1; RRM2B; NT5E; POLD1; NME1 Parkinson's Signaling UCHL1;MAPK8; MAPK13; MAPK14; CASP9; PARK7; PARK2; CASP3 Cardiac & Beta GNAS;GNAQ; PPP2R1A; GNB2L1; PPP2CA; PPP1CC; Adrenergic Signaling PPP2R5CGlycolysis/Gluconeo- HK2; GCK; GPI; ALDH1A1; PKM2; LDHA; HK1 genesisInterferon IFR1; SOCS1; JAK1; JAK2; IFITM1; STAT1; IFIT3 Signaling SonicHedgehog ARRB2; SMO; GLI2; DYRK1A; GLI1; GSK3B; DYRK1B SignalingGlycerophospholipid PLD1; GRN; GPAM; YWHAZ; SPHK1; SPHK2 MetabolismPhospholipid PRDX6; PLD1; GRN; YWHAZ; SPHK1; SPHK2 DegradationTryptophan Metabolism SIAH2; PRMT5; NEDD4; ALDH1A1; CYP1B1; SIAH1 LysineDegradation SUV39H1; EHMT2; NSD1; SETD7; PPP2R5C Nucleotide ExcisionERCC5; ERCC4; XPA; XPC; ERCC1 Repair Pathway Starch and Sucrose UCHL1;HK2; GCK; GPI; HK1 Metabolism Aminosugars Metabolism NQO1; HK2; GCK; HK1Arachidonic Acid PRDX6; GRN; YWHAZ; CYP1B1 Metabolism Circadian RhythmCSNK1E; CREB1; ATF4; NR1D1 Signaling Coagulation System BDKRB1; F2R;SERPINE1; F3 Dopamine Receptor PPP2R1A; PPP2CA; PPP1CC; PPP2R5CSignaling Glutathione Metabolism IDH2; GSTP1; ANPEP; IDH1 GlycerolipidMetabolism ALDH1A1; GPAM; SPHK1; SPHK2 Linoleic Acid PRDX6; GRN; YWHAZ;CYP1B1 Metabolism Methionine Metabolism DNMT1; DNMT3B; AHCY; DNMT3APyruvate Metabolism GLO1; ALDR1A1; PKM2; LDHA Arginine and ProlineALDH1A1; NOS3; NOS2A Metabolism Eicosanoid Signaling PRDX6; GRN; YWHAZFructose and Mannose HK2; GCK; HK1 Metabolism Galactose Metabolism HK2;GCK; HK1 Stilbene, Cournarine and PRDX6; PRDX1; TYR Lignin BiosynthesisAntigen Presentation CALR; B2M Pathway Biosynthesis of Steroids NQO1;DFICR7 Butanoate Metabolism ALDH1A1; NLGN1 Citrate Cycle IDH2; IDH1Fatty Acid Metabolism ALDH1A1; CYP1B1 G ycerophospholipid PRDX6; CHKAMetabolism Histidine Metabolism PRMT5; ALDH1A1 inositol MetabolismERO1L; APEX1 Metabolism of GSTP1; CYP1B1 Xenobiotics by Cytochrome p450Methane Metabolism PRDX6; PRDX1 Phenylalanine PRDX6; PRDX1 MetabolismPropanoate Metabolism ALDHI1A1; LDHA Selenoamino Acid PRMT5; AHCYMetabolism Sphingolipid Metabolism SPHK1; SPFIK2 Aminophosphonate PRMT5Metabolism Androgen and Estrogen PRMT5 Metabolism Ascorbate and AldarateALDH1A1 Metabolism Bile Acid Biosynthesis ALDH1A1 Cysteine MetabolismLDHA Fatty Acid Biosynthesis FASN Glutamate Receptor GNB2L1 SignalingNRF2-mediated PRDX1 Oxidative Stress Response Pentose Phosphate GPIPathway Pentose and Glucuronate UCHL1 Interconversions RetinolMetabolism ALDH1A1 Riboflavin Metabolism TYR Tyrosine Metabolism PRMT5,TYR Ubiquinone Biosynthesis PRMT5 Valine, Leucine and ALDH1A1 IsoleucineDegradation Glycine, Serine and CHKA Threonine Metabolism LysineDegradation ALDH1A1 Pain/Taste TRPM5; TRPA1 Pain TRPM7; TRPC5; TRPC6;TRPC1; Cnrl; cnr2; Grk2; Trpa1; Pomc; Cgrp; Crf; Pka; Era; Nr2b; TRPM5;Prkaca; Prkacb; Prkar1a; Prkar2a Mitochondrial Function AIF; CytC; SMAC(Diablo); Aifm-1; Aifm-2 Developmental BMP-4; Chordin (Chrd); Noggin(Nog); WNT (Wnt2; Neurology Wnt2b; Wnt3a; Wnt4; Wnt5a; Wnt6; Wnt7b;Wnt8b; Wnt9a; Wnt9b; Wnt10a; Wnt10b; Wnt16); beta-catenin; Dkk-1;Frizzled related proteins; Otx-2; Gbx2; FGF-8; Reelin; Dab1; unc-86(Pou4fl or Brn3a); Numb; Reln

Embodiments of the invention also relate to methods and compositionsrelated to knocking out genes, amplifying genes and repairing particularmutations associated with DNA repeat instability and neurologicaldisorders (Robert D. Wells, Tetsuo Ashizawa, Genetic Instabilities andNeurological Diseases, Second Edition, Academic Press, Oct. 13,2011—Medical). Specific aspects of tandem repeat sequences have beenfound to be responsible for more than twenty human diseases (Newinsights into repeat instability: role of RNA*DNA hybrids. Mclvor E I,Polak U. Napierala M. RNA Biol. 2010 September-October; 7(5):551-8). TheCRISPR-Cas system may be harnessed to correct these defects of genomicinstability.

A further aspect of the invention relates to utilizing the CRISPR-Cassystem for correcting defects in the EMP2A and EMP2B genes that havebeen identified to be associated with Lafora disease. Lafora disease isan autosomal recessive condition which is characterized by progressivemyoclonus epilepsy which may start as epileptic seizures in adolescence.A few cases of the disease may be caused by mutations in genes yet to beidentified. The disease causes seizures, muscle spasms, difficultywalking, dementia, and eventually death. There is currently no therapythat has proven effective against disease progression. Other geneticabnormalities associated with epilepsy may also be targeted by theCRISPR-Cas system and the underlying genetics is further described inGenetics of Epilepsy and Genetic Epilepsies, edited by GiulianoAvanzini, Jeffrey L. Noebels, Mariani Foundation Paediatric Neurology:20; 2009).

The methods of US Patent Publication No. 20110158957 assigned to SangamoBioSciences, Inc. involved in inactivating T cell receptor (TCR) genesmay also be modified to the CRISPR Cas system of the present invention.In another example, the methods of US Patent Publication No. 20100311124assigned to Sangamo BioSciences. Inc. and US Patent Publication No.20110225664 assigned to Cellectis, which are both involved ininactivating glutamine synthetase gene expression genes may also bemodified to the CRISPR Cas system of the present invention.

Several further aspects of the invention relate to correcting defectsassociated with a wide range of genetic diseases which are furtherdescribed on the website of the National Institutes of Health under thetopic subsection Genetic Disorders (website athealth.nih.gov/topic/GeneticDisorders). The genetic brain diseases mayinclude but are not limited to Adrenoleukodystrophy, Agenesis of theCorpus Callosum, Aicardi Syndrome, Alpers' Disease, Alzheimer's Disease,Barth Syndrome, Batten Disease, CADASIL, Cerebellar Degeneration,Fabry's Disease, Gerstmann-Straussler-Scheinker Disease, Huntington'sDisease and other Triplet Repeat Disorders, Leigh's Disease, Lesch-NyhanSyndrome, Menkes Disease, Mitochondrial Myopathies and NINDSColpocephaly. These diseases are further described on the website of theNational Institutes of Health under the subsection Genetic BrainDisorders.

In some embodiments, the condition may be neoplasia. In someembodiments, where the condition is neoplasia, the genes to be targetedare any of those listed in Table A (in this case PTEN and so forth). Insome embodiments, the condition may be Age-related Macular Degeneration.In some embodiments, the condition may be a Schizophrenic Disorder. Insome embodiments, the condition may be a Trinucleotide Repeat Disorder.In some embodiments, the condition may be Fragile X Syndrome. In someembodiments, the condition may be a Secretase Related Disorder. In someembodiments, the condition may be a Prion-related disorder. In someembodiments, the condition may be ALS. In some embodiments, thecondition may be a drug addiction. In some embodiments, the conditionmay be Autism. In some embodiments, the condition may be Alzheimer'sDisease. In some embodiments, the condition may be inflammation. In someembodiments, the condition may be Parkinson's Disease.

For example, US Patent Publication No. 20110023145, describes use ofzinc finger nucleases to genetically modify cells, animals and proteinsassociated with autism spectrum disorders (ASD). Autism spectrumdisorders (ASDs) are a group of disorders characterized by qualitativeimpairment in social interaction and communication, and restrictedrepetitive and stereotyped patterns of behavior, interests, andactivities. The three disorders, autism, Asperger syndrome (AS) andpervasive developmental disorder-not otherwise specified (PDD-NOS) are acontinuum of the same disorder with varying degrees of severity,associated intellectual functioning and medical conditions. ASDs arepredominantly genetically determined disorders with a heritability ofaround 90%.

US Patent Publication No. 20110023145 comprises editing of anychromosomal sequences that encode proteins associated with ASD which maybe applied to the CRISPR Cas system of the present invention. Theproteins associated with ASD are typically selected based on anexperimental association of the protein associated with ASD to anincidence or indication of an ASD. For example, the production rate orcirculating concentration of a protein associated with ASD may beelevated or depressed in a population having an ASD relative to apopulation lacking the ASD. Differences in protein levels may beassessed using proteomic techniques including but not limited to Westernblot, immunohistochemical staining, enzyme linked immunosorbent assay(ELISA), and mass spectrometry. Alternatively, the proteins associatedwith ASD may be identified by obtaining gene expression profiles of thegenes encoding the proteins using genomic techniques including but notlimited to DNA microarray analysis, serial analysis of gene expression(SAGE), and quantitative real-time polymerase chain reaction (Q-PCR).

Non limiting examples of disease states or disorders that may beassociated with proteins associated with ASD include autism, Aspergersyndrome (AS), pervasive developmental disorder-not otherwise specified(PDD-NOS), Rett's syndrome, tuberous sclerosis, phenylketonuria,Smith-Lemli-Opitz syndrome and fragile X syndrome. By way ofnon-limiting example, proteins associated with ASD include but are notlimited to the following proteins: ATP10C aminophospholipid-MET METreceptor transporting ATPase tyrosine kinase (ATP10C) BZRAP1 MGLUR5(GRM5) Metabotropic glutamate receptor 5 (MGLUR5) CDH10 Cadherin-10MGLUR6 (GRM6) Metabotropic glutamate receptor 6 (MGLUR6) CDH9 Cadherin-9NLGN1 Neuroligin-1 CNTN4 Contactin-4 NLGN2 Neuroligin-2 CNTNAP2Contactin-associated SEMA5A Neuroligin-3 protein-like 2 (CNTNAP2) DHCR77-dehydrocholesterol NLGN4X Neuroligin-4X-reductase (DHCR7) linked DOC2ADouble C2-like domain—NLGN4Y Neuroligin-4 Y—containing protein alphalinked DPP6 Dipeptidyl NLGN5 Neuroligin-5 aminopeptidase-like protein 6EN2 engrailed 2 (EN2) NRCAM Neuronal cell adhesion molecule (NRCAM)MDGA2 fragile X mental retardation NRXN1 Neurexin-1 1 (MDGA2) FMR2(AFF2) AF4/FMR2 family member 20R4M2 Olfactory receptor (AFF2) 4M2 FOXP2Forkhead box protein P2 OR4N4 Olfactory receptor (FOXP2) 4N4 FXR1FragileX mental OXTR oxytocin receptor retardation, autosomal (OXTR) homolog 1(FXR1) FXR2 Fragile X mental PAH phenylalanine retardation, autosomalhydroxylase (PAH) homolog 2 (FXR2) GABRA1 Gamma-aminobutyric acid PTENPhosphatase and receptor subunit alpha-1 tensin homologue (GABRA1)(PTEN) GABRA5 GABAA (.gamma.-aminobutyric PTPRZ1 Receptor-type acid)receptor alpha 5 tyrosine-protein subunit (GABRAS) phosphatase zeta(PTPRZ1) GABRB1 Gamma-aminobutyric acid RELN Reelin receptor subunitbeta-1 (GABRB1) GABRB3 GABAA (.gamma.-aminobutyric RPL10 60S ribosomalacid) receptor .beta.3 subunit protein L10 (GABRB3) GABRG1Gamma-aminobutyric acid SEMA5A Semaphorin-5A receptor subunit gamma-1(SEMA5A) (GABRG1) HIRIP3 HIRA-interacting protein 3 SEZ6L2 seizurerelated 6 homolog (mouse)-like 2 HOXA1 Homeobox protein Hox-A1 SHANK3SH3 and multiple (HOXA1) ankyrin repeat domains 3 (SHANK3) IL6Interleukin-6 SHBZRAP1 SH3 and multiple ankyrin repeat domains 3(SHBZRAP1) LAMB1 Laminin subunit beta-1 SLC6A4 Serotonin (LAMB1)transporter (SERT) MAPK3 Mitogen-activated protein TAS2R1Taste receptorkinase 3 type 2 member 1 TAS2R1 MAZ Myc-associated zinc finger TSC1Tuberous sclerosis protein protein 1 MDGA2 MAM domain containing TSC2Tuberous sclerosis glycosylphosphatidylinositol protein 2 anchor 2(MDGA2) MECP2 Methyl CpG binding UBE3A Ubiquitin protein protein 2(MECP2) ligase E3A (UBE3A) MECP2 methyl CpG binding WNT2 Wingless-typeprotein 2 (MECP2) MMTV integration site family, member 2 (WNT2)

The identity of the protein associated with ASD whose chromosomalsequence is edited can and will vary. In preferred embodiments, theproteins associated with ASD whose chromosomal sequence is edited may bethe benzodiazapine receptor (peripheral) associated protein 1 (BZRAP1)encoded by the BZRAP1 gene, the AF4/FMR2 family member 2 protein (AFF2)encoded by the AFF2 gene (also termed MFR2), the fragile X mentalretardation autosomal homolog 1 protein (FXR1) encoded by the FXR1 gene,the fragile X mental retardation autosomal homolog 2 protein (FXR2)encoded by the FXR2 gene, the MAM domain containingglycosylphosphatidylinositol anchor 2 protein (MDGA2) encoded by theMDGA2 gene, the methyl CpG binding protein 2 (MECP2) encoded by theMECP2 gene, the metabotropic glutamate receptor 5 (MGLURS) encoded bythe MGLUR5-1 gene (also termed GRM5), the neurexin 1 protein encoded bythe NRXN1 gene, or the semaphorin-5A protein (SEMA5A) encoded by theSEMA5A gene. In an exemplary embodiment, the genetically modified animalis a rat, and the edited chromosomal sequence encoding the proteinassociated with ASD is as listed below: BZRAP1 benzodiazapine receptorXM_(—)002727789, (peripheral) associated XM_(—)213427, protein 1(BZRAP1) XM_(—)002724533, XM_(—)001081125 AFF2 (FMR2) AF4/FMR2 familymember 2 XM_(—)219832, (AFF2) XM_(—)001054673 FXR1Fragile X mentalNM_(—)001012179 retardation, autosomal homolog 1 (FXR1) FXR2Fragile Xmental NM_(—)001100647 retardation, autosomal homolog 2 (FXR2) MDGA2 MAMdomain containing NM_(—)199269 glycosylphosphatidylinositol anchor 2(MDGA2) MECP2 Methyl CpG binding NM_(—)022673 protein 2 (MECP2)MGLUR5Metabotropic glutamate NM_(—)017012 (GRM5) receptor 5 (MGLUR5)NRXN1 Neurexin-1 NM_(—)021767 SEMA5A Semaphorin-5A (SEMA5A)NM_(—)001107659

Exemplary animals or cells may comprise one, two, three, four, five,six, seven, eight, or nine or more inactivated chromosomal sequencesencoding a protein associated with ASD, and zero, one, two, three, four,five, six, seven, eight, nine or more chromosomally integrated sequencesencoding proteins associated with ASD. The edited or integratedchromosomal sequence may be modified to encode an altered proteinassociated with ASD. Non-limiting examples of mutations in proteinsassociated with ASD include the L18Q mutation in neurexin 1 where theleucine at position 18 is replaced with a glutamine, the R451c mutationin neuroligin 3 where the arginine at position 451 is replaced with acysteine, the R87W mutation in neuroligin 4 where the arginine atposition 87 is replaced with a tryptophan, and the I425V mutation inserotonin transporter where the isoleucine at position 425 is replacedwith a valine. A number of other mutations and chromosomalrearrangements in ASD-related chromosomal sequences have been associatedwith ASD and are known in the art. See, for example, Freitag et al.(2010) Eur. Child. Adolesc. Psychiatry 19:169-178, and Bucan et al.(2009) PLoS Genetics 5: e1000536, the disclosure of which isincorporated by reference herein in its entirety.

Examples of proteins associated with Parkinson's disease include but arenot limited to α-synuclein, DJ-1, LRRK2, PINK1, Parkin, UCHL1,Synphilin-1, and NURR1.

Examples of addiction-related proteins may include ABAT for example.

Examples of inflammation-related proteins may include the monocytechemoattractant protein-1 (MCP1) encoded by the Ccr2 gene, the C-Cchemokine receptor type 5 (CCR5) encoded by the Ccr5 gene, the IgGreceptor IIB (FCGR2b, also termed CD32) encoded by the Fcgr2b gene, orthe Fc epsilon R1g (FCER1g) protein encoded by the Fcer1g gene, forexample.

Examples of cardiovascular diseases associated proteins may include IL1B(interleukin 1, beta), XDH (xanthine dehydrogenase), TP53 (tumor proteinp53), PTGIS (prostaglandin 12 (prostacyclin) synthase). MB (myoglobin),IL4 (interleukin 4), ANGPT1 (angiopoietin 1), ABCG8 (ATP-bindingcassette, sub-family G (WHITE), member 8), or CTSK (cathepsin K), forexample.

For example, US Patent Publication No. 20110023153, describes use ofzinc finger nucleases to genetically modify cells, animals and proteinsassociated with Alzheimer's Disease. Once modified cells and animals maybe further tested using known methods to study the effects of thetargeted mutations on the development and/or progression of AD usingmeasures commonly used in the study of AD—such as, without limitation,learning and memory, anxiety, depression, addiction, and sensory motorfunctions as well as assays that measure behavioral, functional,pathological, metaboloic and biochemical function.

The present disclosure comprises editing of any chromosomal sequencesthat encode proteins associated with AD. The AD-related proteins aretypically selected based on an experimental association of theAD-related protein to an AD disorder. For example, the production rateor circulating concentration of an AD-related protein may be elevated ordepressed in a population having an AD disorder relative to a populationlacking the AD disorder. Differences in protein levels may be assessedusing proteomic techniques including but not limited to Western blot,immunohistochemical staining, enzyme linked immunosorbent assay (ELISA),and mass spectrometry. Alternatively, the AD-related proteins may beidentified by obtaining gene expression profiles of the genes encodingthe proteins using genomic techniques including but not limited to DNAmicroarray analysis, serial analysis of gene expression (SAGE), andquantitative real-time polymerase chain reaction (Q-PCR).

Examples of Alzheimer's disease associated proteins may include the verylow density lipoprotein receptor protein (VLDLR) encoded by the VLDLRgene, the ubiquitin-like modifier activating enzyme 1 (UBA1) encoded bythe UBA1 gene, or the NEDD8-activating enzyme E1 catalytic subunitprotein (UBE1C) encoded by the UBA3 gene, for example.

By way of non-limiting example, proteins associated with AD include butare not limited to the proteins listed as follows: Chromosomal SequenceEncoded Protein ALAS2 Delta-aminolevulinate synthase 2 (ALAS2) ABCA1ATP-binding cassette transporter (ABCA1) ACE Angiotensin 1-convertingenzyme (ACE) APOE Apolipoprotein E precursor (APOE) APP amyloidprecursor protein (APP) AQP1 aquaporin 1 protein (AQP1) BIN1 Mycbox-dependent-interacting protein 1 or bridging integrator 1 protein(BIN1) BDNF brain-derived neurotrophic factor (BDNF) BTNL8Butyrophilin-like protein 8 (BTNL8) C1ORF49 chromosome 1 open readingframe 49 CDH4 Cadherin-4 CHRNB2 Neuronal acetylcholine receptor subunitbeta-2 CKLFSF2 CKLF-like MARVEL transmembrane domain-containing protein2 (CKLFSF2) CLEC4E C-type lectin domain family 4, member e (CLEC4E) CLUclusterin protein (also known as apoplipoprotein J) CR1 Erythrocytecomplement receptor 1 (CR1, also known as CD35, C3b/C4b receptor andimmune adherence receptor) CR1L Erythrocyte complement receptor 1 (CR1L)CSF3R granulocyte colony-stimulating factor 3 receptor (CSF3R) CST3Cystatin C or cystatin 3 CYP2C Cytochrome P450 2C DAPK1 Death-associatedprotein kinase 1 (DAPK1) ESR1 Estrogen receptor 1 FCAR Fc fragment ofIgA receptor (FCAR, also known as CD89) FCGR3B Fc fragment of IgG, lowaffinity IIIb, receptor (FCGR3B or CD16b) FFA2 Free fatty acid receptor2 (FFA2) FGA Fibrinogen (Factor I) GAB2 GRB2-associated-binding protein2 (GAB2) GAB2 GRB2-associated-binding protein 2 (GAB2) GALP Galanin-likepeptide GAPDHS Glyceraldehyde-3-phosphate dehydrogenase, spermatogenic(GAPDHS) GMPB GMBP HP Haptoglobin (HP) HTR75-hydroxytryptamine(serotonin) receptor 7 (adenylate cyclase-coupled) IDE Insulin degradingenzyme IF127 IF127 IF16 Interferon, alpha-inducible protein 6 (IF16)IFIT2 Interferon-induced protein with tetratricopeptide repeats 2(IFIT2) IL1RN interleukin-1 receptor antagonist (IL-RA) IL8RAInterleukin 8 receptor, alpha (IL8RA or CD181) IL8RB Interleukin 8receptor, beta (IL8RB) JAG1 Jagged 1 (JAG1) KCNJ15 Potassiuminwardly-rectifying channel, subfamily J, member 15 (KCNJ15) LRP6Low-density lipoprotein receptor-related protein 6 (LRP6) MAPTmicrotubule-associated protein tau (MAPT) MARK4 MAP/microtubuleaffinity-regulating kinase 4 (MARK4) MPHOSPH1 M-phase phosphoprotein 1MTHFR 5,10-methylenetetrahydrofolate reductase MX2 Interferon-inducedGTP-binding protein Mx2 NBN Nibrin, also known as NBN NCSTN NicastrinNIACR2 Niacin receptor 2 (NIACR2, also known as GPR109B) NMNAT3nicotinamide nucleotide adenylyltransferase 3 NTM Neurotrimin (or HNT)ORM1 Orosmucoid 1 (ORM1) or Alpha-1-acid glycoprotein 1 P2RY13 P2Ypurinoceptor 13 (P2RY13) PBEF1 Nicotinamide phosphoribosyltransferase(NAmPRTase or Nampt) also known as pre-B-cell colony-enhancing factor 1(PBEF1) or visfatin PCK1 Phosphoenolpyruvate carboxykinase PICALMphosphatidylinositol binding clathrin assembly protein (PICALM) PLAUUrokinase-type plasminogen activator (PLAU) PLXNC1 Plexin C1 (PLXNC1)PRNP Prion protein PSEN1 presenilin 1 protein (PSEN1) PSEN2 presenilin 2protein (PSEN2) PTPRA protein tyrosine phosphatase receptor type Aprotein (PTPRA) RALGPS2 RAl GEF with PH domain and SH3 binding motif 2(RALGPS2) RGSL2 regulator of G-protein signaling like 2 (RGSL2) SELENBP1Selenium binding protein 1 (SELNBP1) SLC25A37 Mitoferrin-1 SORL1sortilin-related receptor L(DLR class) A repeats-containing protein(SORL1) TF Transferrin TFAM Mitochondrial transcription factor A TNFTumor necrosis factor TNFRSF10C Tumor necrosis factor receptorsuperfamily member 10C (TNFRSF10C) TNFSF10 Tumor necrosis factorreceptor superfamily, (TRAIL) member 10a (TNFSF10) UBA1 ubiquitin-likemodifier activating enzyme 1 (UBA1) UBA3 NEDD8-activating enzyme E1catalytic subunit protein (UBE1C) UBB ubiquitin B protein (UBB) UBQLN1Ubiquilin-1 UCHL1 ubiquitin carboxyl-terminal esterase L1 protein(UCHL1) UCHL3 ubiquitin carboxyl-terminal hydrolase isozyme L3 protein(UCHL3) VLDLR very low density lipoprotein receptor protein (VLDLR)

In exemplary embodiments, the proteins associated with AD whosechromosomal sequence is edited may be the very low density lipoproteinreceptor protein (VLDLR) encoded by the VLDLR gene, the ubiquitin-likemodifier activating enzyme 1 (UBA1) encoded by the UBA1 gene, theNEDD8-activating enzyme E1 catalytic subunit protein (UBE1C) encoded bythe UBA3 gene, the aquaporin 1 protein (AQP1) encoded by the AQP1 gene,the ubiquitin carboxyl-terminal esterase L1 protein (UCHL1) encoded bythe UCHL1 gene, the ubiquitin carboxyl-terminal hydrolase isozyme L3protein (UCHL3) encoded by the UCHL3 gene, the ubiquitin B protein (UBB)encoded by the UBB gene, the microtubule-associated protein tau (MAPT)encoded by the MAPT gene, the protein tyrosine phosphatase receptor typeA protein (PTPRA) encoded by the PTPRA gene, the phosphatidylinositolbinding clathrin assembly protein (PICALM) encoded by the PICALM gene,the clusterin protein (also known as apoplipoprotein J) encoded by theCLU gene, the presenilin 1 protein encoded by the PSEN1 gene, thepresenilin 2 protein encoded by the PSEN2 gene, the sortilin-relatedreceptor L(DLR class) A repeats-containing protein (SORL1) proteinencoded by the SORL1 gene, the amyloid precursor protein (APP) encodedby the APP gene, the Apolipoprotein E precursor (APOE) encoded by theAPOE gene, or the brain-derived neurotrophic factor (BDNF) encoded bythe BDNF gene. In an exemplary embodiment, the genetically modifiedanimal is a rat, and the edited chromosomal sequence encoding theprotein associated with AD is as as follows: APP amyloid precursorprotein (APP) NM_(—)019288 AQP1 aquaporin 1 protein (AQP1) NM_(—)012778BDNF Brain-derived neurotrophic factor NM_(—)012513 CLU clusterinprotein (also known as NM_(—)053021 apoplipoprotein J) MAPTmicrotubule-associated protein NM_(—)017212 tau (MAPT) PICALMphosphatidylinositol binding NM_(—)053554 clathrin assembly protein(PICALM) PSEN1 presenilin 1 protein (PSEN1) NM_(—)019163 PSEN2presenilin 2 protein (PSEN2) NM_(—)031087 PTPRA protein tyrosinephosphatase NM_(—)012763 receptor type A protein (PTPRA) SOR1sortilin-related receptor L(DLR NM_(—)053519, class) Arepeats-containing XM_(—)001065506, protein (SORL1) XM_(—)217115 UBA1ubiquitin-like modifier activating NM_(—)001014080 enzyme 1 (UBA1) UBA3NEDD8-activating enzyme E1 NM_(—)057205 catalytic subunit protein(UBE1C) UBB ubiquitin B protein (UBB) NM_(—)138895 UCHL1 ubiquitincarboxyl-terminal NM_(—)017237 esterase L1 protein (UCHL1) UCHL3ubiquitin carboxyl-terminal NM_(—)001110165 hydrolase isozyme L3 protein(UCHL3) VLDLR very low density lipoprotein NM_(—)013155 receptor protein(VLDLR)

The animal or cell may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15 or more disrupted chromosomal sequences encoding a proteinassociated with AD and zero, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15 or more chromosomally integrated sequences encoding a proteinassociated with AD.

The edited or integrated chromosomal sequence may be modified to encodean altered protein associated with AD. A number of mutations inAD-related chromosomal sequences have been associated with AD. Forinstance, the V7171 (i.e. valine at position 717 is changed toisoleucine) missense mutation in APP causes familial AD. Multiplemutations in the presenilin-1 protein, such as H163R (i.e. histidine atposition 163 is changed to arginine), A246E (i.e. alanine at position246 is changed to glutamate), L286V (i.e. leucine at position 286 ischanged to valine) and C410Y (i.e. cysteine at position 410 is changedto tyrosine) cause familial Alzheimer's type 3. Mutations in thepresenilin-2 protein, such as N141 I (i.e. asparagine at position 141 ischanged to isoleucine), M239V (i.e. methionine at position 239 ischanged to valine), and D439A (i.e. aspartate at position 439 is changedto alanine) cause familial Alzheimer's type 4. Other associations ofgenetic variants in AD-associated genes and disease are known in theart. See, for example, Waring et al. (2008) Arch. Neurol. 65:329-334,the disclosure of which is incorporated by reference herein in itsentirety.

Examples of proteins associated Autism Spectrum Disorder may include thebenzodiazapine receptor (peripheral) associated protein 1 (BZRAP1)encoded by the BZRAP1 gene, the AF4/FMR2 family member 2 protein (AFF2)encoded by the AFF2 gene (also termed MFR2), the fragile X mentalretardation autosomal homolog 1 protein (FXR1) encoded by the FXR1 gene,or the fragile X mental retardation autosomal homolog 2 protein (FXR2)encoded by the FXR2 gene, for example.

Examples of proteins associated Macular Degeneration may include theATP-binding cassette, sub-family A (ABC1) member 4 protein (ABCA4)encoded by the ABCR gene, the apolipoprotein E protein (APOE) encoded bythe APOE gene, or the chemokine (C-C motif) Ligand 2 protein (CCL2)encoded by the CCL2 gene, for example.

Examples of proteins associated Schizophrenia may include NRG1, ErbB4,CPLX1, TPH1, TPH2, NRXN1, GSK3A, BDNF, DISC1, GSK3B, and combinationsthereof.

Examples of proteins involved in tumor suppression may include ATM(ataxia telangiectasia mutated), ATR (ataxia telangiectasia and Rad3related), EGFR (epidermal growth factor receptor), ERBB2 (v-erb-b2erythroblastic leukemia viral oncogene homolog 2), ERBB3 (v-erb-b2erythroblastic leukemia viral oncogene homolog 3), ERBB4 (v-erb-b2erythroblastic leukemia viral oncogene homolog 4), Notch 1, Notch2,Notch 3, or Notch 4, for example.

Examples of proteins associated with a secretase disorder may includePSENEN (presenilin enhancer 2 homolog (C. elegans)), CTSB (cathepsin B),PSEN1 (presenilin 1), APP (amyloid beta (A4) precursor protein), APH1B(anterior pharynx defective I homolog B (C. elegans)), PSEN2 (presenilin2 (Alzheimer disease 4)), or BACE (beta-site APP-cleaving enzyme 1), forexample.

For example, US Patent Publication No. 20110023146, describes use ofzinc finger nucleases to genetically modify cells, animals and proteinsassociated with secretase-associated disorders. Secretases are essentialfor processing pre-proteins into their biologically active forms.Defects in various components of the secretase pathways contribute tomany disorders, particularly those with hallmark amyloidogenesis oramyloid plaques, such as Alzheimer's disease (AD).

A secretase disorder and the proteins associated with these disordersare a diverse set of proteins that effect susceptibility for numerousdisorders, the presence of the disorder, the severity of the disorder,or any combination thereof. The present disclosure comprises editing ofany chromosomal sequences that encode proteins associated with asecretase disorder. The proteins associated with a secretase disorderare typically selected based on an experimental association of thesecretase-related proteins with the development of a secretase disorder.For example, the production rate or circulating concentration of aprotein associated with a secretase disorder may be elevated ordepressed in a population with a secretase disorder relative to apopulation without a secretase disorder. Differences in protein levelsmay be assessed using proteomic techniques including but not limited toWestern blot, immunohistochemical staining, enzyme linked immunosorbentassay (ELISA), and mass spectrometry. Alternatively, the proteinassociated with a secretase disorder may be identified by obtaining geneexpression profiles of the genes encoding the proteins using genomictechniques including but not limited to DNA microarray analysis, serialanalysis of gene expression (SAGE), and quantitative real-timepolymerase chain reaction (Q-PCR).

By way of non-limiting example, proteins associated with a secretasedisorder include PSENEN (presenilin enhancer 2 homolog (C. elegans)),CTSB (cathepsin B), PSEN1 (presenilin 1), APP (amyloid beta (A4)precursor protein), APH1B (anterior pharynx defective 1 homolog B (C.elegans)), PSEN2 (presenilin 2 (Alzheimer disease 4)), BACE1 (beta-siteAPP-cleaving enzyme 1), ITM2B (integral membrane protein 2B), CTSD(cathepsin D), NOTCH1 (Notch homolog 1, translocation-associated(Drosophila)), TNF (tumor necrosis factor (TNF superfamily, member 2)),INS (insulin), DYT10 (dystonia 10), ADAM17 (ADAM metallopeptidase domain17), APOE (apolipoprotein E), ACE (angiotensin I converting enzyme(peptidyl-dipeptidase A) 1), STN (statin), TP53 (tumor protein p53), IL6(interleukin 6 (interferon, beta 2)), NGFR (nerve growth factor receptor(TNFR superfamily, member 16)), IL1B (interleukin 1, beta), ACHE(acetylcholinesterase (Yt blood group)), CTNNB1 (catenin(cadherin-associated protein), beta 1, 88 kDa), IGF1 (insulin-likegrowth factor 1 (somatomedin C)), IFNG (interferon, gamma), NRG1(neuregulin 1), CASP3 (caspase 3, apoptosis-related cysteine peptidase),MAPK1 (mitogen-activated protein kinase 1), CDH1 (cadherin 1, type 1,E-cadherin (epithelial)), APBB1 (amyloid beta (A4) precursorprotein-binding, family B, member 1 (Fe65)), HMGCR(3-hydroxy-3-methylglutaryl-Coenzyme A reductase). CREB1 (cAMPresponsive element binding protein 1), PTGS2 (prostaglandin-endoperoxidesynthase 2 (prostaglandin G/H synthase and cyclooxygenase)), HES1 (hairyand enhancer of split 1, (Drosophila)), CAT (catalase), TGFB1(transforming growth factor, beta 1), ENO2 (enolase 2 (gamma,neuronal)), ERBB4 (v-erb-a erythroblastic leukemia viral oncogenehomolog 4 (avian)), TRAPPC10 (trafficking protein particle complex 10),MAOB (monoamine oxidase B), NGF (nerve growth factor (betapolypeptide)), MMP12 (matrix metallopeptidase 12 (macrophage elastase)),JAG1 (jagged 1 (Alagille syndrome)), CD40LG (CD40 ligand), PPARG(peroxisome proliferator-activated receptor gamma), FGF2 (fibroblastgrowth factor 2 (basic)), IL3 (interleukin 3 (colony-stimulating factor,multiple)), LRP1 (low density lipoprotein receptor-related protein 1),NOTCH4 (Notch homolog 4 (Drosophila)), MAPK8 (mitogen-activated proteinkinase 8), PREP (prolyl endopeptidase), NOTCH3 (Notch homolog 3(Drosophila)), PRNP (prion protein), CTSG (cathepsin G), EGF (epidermalgrowth factor (beta-urogastrone)), REN (renin), CD44 (CD44 molecule(Indian blood group)), SELP (selectin P (granule membrane protein 140kDa, antigen CD62)), GHR (growth hormone receptor), ADCYAP1 (adenylatecyclase activating polypeptide 1 (pituitary)), INSR (insulin receptor),GFAP (glial fibrillary acidic protein), MMP3 (matrix metallopeptidase 3(stromelysin 1, progelatinase)), MAPK10 (mitogen-activated proteinkinase 10), SP (Sp 1 transcription factor), MYC (v-myc myelocytomatosisviral oncogene homolog (avian)), CTSE (cathepsin E), PPARA (peroxisomeproliferator-activated receptor alpha), JUN (jun oncogene), TIMP1 (TIMPmetallopeptidase inhibitor 1), IL5 (interleukin 5 (colony-stimulatingfactor, eosinophil)), IL1A (interleukin 1, alpha), MMP9 (matrixmetallopeptidase 9 (gelatinase B, 92 kDa gelatinase, 92 kDa type IVcollagenase)), HTR4 (5-hydroxytryptamine (serotonin) receptor 4), HSPG2(heparan sulfate proteoglycan 2), KRAS (v-Ki-ras2 Kirsten rat sarcomaviral oncogene homolog), CYCS (cytochrome c, somatic), SMG1 (SMG1homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)),IL1R1 (interleukin 1 receptor, type 1), PROK1 (prokineticin 1), MAPK3(mitogen-activated protein kinase 3), NTRK1 (neurotrophic tyrosinekinase, receptor, type 1), IL13 (interleukin 13), MME (membranemetallo-endopeptidase), TKT (transketolase), CXCR2 (chemokine (C-X-Cmotif) receptor 2), IGF1R (insulin-like growth factor 1 receptor), RARA(retinoic acid receptor, alpha), CREBBP (CREB binding protein), PTGS1(prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase andcyclooxygenase)), GALT (galactose-1-phosphate uridylyltransferase),CHRM1 (cholinergic receptor, muscarinic 1), ATXN1 (ataxin 1), PAWR(PRKC, apoptosis, WT1, regulator), NOTCH2 (Notch homolog 2(Drosophila)), M6PR (mannose-6-phosphate receptor (cation dependent)),CYP46A1 (cytochrome P450, family 46, subfamily A, polypeptide 1), CSNK1D (casein kinase 1, delta), MAPK14 (mitogen-activated protein kinase14), PRG2 (proteoglycan 2, bone marrow (natural killer cell activator,eosinophil granule major basic protein)), PRKCA (protein kinase C,alpha), L1 CAM (L1 cell adhesion molecule), CD40 (CD40 molecule, TNFreceptor superfamily member 5), NR1I2 (nuclear receptor subfamily 1,group I, member 2), JAG2 (jagged 2), CTNND1 (catenin(cadherin-associated protein), delta 1), CDH2 (cadherin 2, type 1,N-cadherin (neuronal)), CMA1 (chymase 1, mast cell), SORT1 (sortilin 1),DLK1 (delta-like 1 homolog (Drosophila)), THEM4 (thioesterasesuperfamily member 4), JUP (junction plakoglobin), CD46 (CD46 molecule,complement regulatory protein), CCL11 (chemokine (C-C motif) ligand 11),CAV3 (caveolin 3), RNASE3 (ribonuclease, RNase A family, 3 (eosinophilcationic protein)), HSPA8 (heat shock 70 kDa protein 8), CASP9 (caspase9, apoptosis-related cysteine peptidase), CYP3A4 (cytochrome P450,family 3, subfamily A, polypeptide 4), CCR3 (chemokine (C-C motif)receptor 3), TFAP2A (transcription factor AP-2 alpha (activatingenhancer binding protein 2 alpha)), SCP2 (sterol carrier protein 2),CDK4 (cyclin-dependent kinase 4), HIF1A (hypoxia inducible factor 1,alpha subunit (basic helix-loop-helix transcription factor)), TCF7L2(transcription factor 7-like 2 (T-cell specific, HMG-box)), IL1R2(interleukin 1 receptor, type II), B3GALTL (beta1,3-galactosyltransferase-like), MDM2 (Mdm2 p53 binding protein homolog(mouse)), RELA (v-rel reticuloendotheliosis viral oncogene homolog A(avian)), CASP7 (caspase 7, apoptosis-related cysteine peptidase), IDE(insulin-degrading enzyme), FABP4 (fatty acid binding protein 4,adipocyte), CASK (calcium/calmodulin-dependent serine protein kinase(MAGUK family)), ADCYAP1R1 (adenylate cyclase activating polypeptide 1(pituitary) receptor type I), ATF4 (activating transcription factor 4(tax-responsive enhancer element B67)), PDGFA (platelet-derived growthfactor alpha polypeptide), C21 or f33 (chromosome 21 open reading frame33), SCG5 (secretogranin V (7B2 protein)), RNF123 (ring finger protein123), NFKB1 (nuclear factor of kappa light polypeptide gene enhancer inB-cells 1), ERBB2 (v-erb-b2 erythroblastic leukemia viral oncogenehomolog 2, neuro/glioblastoma derived oncogene homolog (avian)), CAV1(caveolin 1, caveolae protein, 22 kDa), MMP7 (matrix metallopeptidase 7(matrilysin, uterine)), TGFA (transforming growth factor, alpha), RXRA(retinoid X receptor, alpha), STX1A (syntaxin 1A (brain)), PSMC4(proteasome (prosome, macropain) 26S subunit, ATPase, 4), P2RY2(purinergic receptor P2Y, G-protein coupled, 2), TNFRSF21 (tumornecrosis factor receptor superfamily, member 21). DLG1 (discs, largehomolog 1 (Drosophila)), NUMBL (numb homolog (Drosophila)-like), SPN(sialophorin), PLSCR1 (phospholipid scramblase 1), UBQLN2 (ubiquilin 2),UBQLN1 (ubiquilin 1), PCSK7 (proprotein convertase subtilisin/kexin type7), SPON1 (spondin 1, extracellular matrix protein), SILV (silverhomolog (mouse)), QPCT (glutaminyl-peptide cyclotransferase), HESS(hairy and enhancer of split 5 (Drosophila)), GCC1 (GRIP and coiled-coildomain containing 1), and any combination thereof.

The genetically modified animal or cell may comprise 1, 2, 3, 4, 5, 6,7, 8, 9, 10 or more disrupted chromosomal sequences encoding a proteinassociated with a secretase disorder and zero, 1, 2, 3, 4, 5, 6, 7, 8,9, 10 or more chromosomally integrated sequences encoding a disruptedprotein associated with a secretase disorder.

Examples of proteins associated with Amyotrophic Lateral Sclerosis mayinclude SOD1 (superoxide dismutase 1), ALS2 (amyotrophic lateralsclerosis 2), FUS (fused in sarcoma), TARDBP (TAR DNA binding protein),VAGFA (vascular endothelial growth factor A), VAGFB (vascularendothelial growth factor B), and VAGFC (vascular endothelial growthfactor C), and any combination thereof.

For example, US Patent Publication No. 20110023144, describes use ofzinc finger nucleases to genetically modify cells, animals and proteinsassociated with amyotrophyic lateral sclerosis (ALS) disease. ALS ischaracterized by the gradual steady degeneration of certain nerve cellsin the brain cortex, brain stem, and spinal cord involved in voluntarymovement.

Motor neuron disorders and the proteins associated with these disordersare a diverse set of proteins that effect susceptibility for developinga motor neuron disorder, the presence of the motor neuron disorder, theseverity of the motor neuron disorder or any combination thereof. Thepresent disclosure comprises editing of any chromosomal sequences thatencode proteins associated with ALS disease, a specific motor neurondisorder. The proteins associated with ALS are typically selected basedon an experimental association of ALS-related proteins to ALS. Forexample, the production rate or circulating concentration of a proteinassociated with ALS may be elevated or depressed in a population withALS relative to a population without ALS. Differences in protein levelsmay be assessed using proteomic techniques including but not limited toWestern blot, immunohistochemical staining, enzyme linked immunosorbentassay (ELISA), and mass spectrometry. Alternatively, the proteinsassociated with ALS may be identified by obtaining gene expressionprofiles of the genes encoding the proteins using genomic techniquesincluding but not limited to DNA microarray analysis, serial analysis ofgene expression (SAGE), and quantitative real-time polymerase chainreaction (Q-PCR).

By way of non-limiting example, proteins associated with ALS include butare not limited to the following proteins: SOD1 superoxide dismutase 1,ALS3 amyotrophic lateral soluble sclerosis 3 SETX senataxin ALS5amyotrophic lateral sclerosis 5 FUS fused in sarcoma ALS7 amyotrophiclateral sclerosis 7 ALS2 amyotrophic lateral DPP6 Dipeptidyl-peptidase 6sclerosis 2 NEFH neurofilament, heavy PTGS1 prostaglandin-polypeptideendoperoxide synthase 1 SLC1A2 solute carrier family 1 TNFRSF10B tumornecrosis factor (glial high affinity receptor superfamily, glutamatetransporter), member 10b member 2 PRPH peripherin HSP90AA1 heat shockprotein 90 kDa alpha (cytosolic), class A member 1 GRIA2 glutamatereceptor, IFNG interferon, gamma ionotropic, AMPA 2 S100B S100 calciumbinding FGF2 fibroblast growth factor 2 protein B AOX1 aldehyde oxidase1 CS citrate synthase TARDBP TAR DNA binding protein TXN thioredoxinRAPH1 Ras association MAP3K5 mitogen-activated protein (RaIGDS/AF-6) andkinase 5 pleckstrin homology domains 1 NBEAL1 neurobeachin-like 1 GPX1glutathione peroxidase 1 ICA1L islet cell autoantigen RAC1 ras-relatedC3 botulinum 1.69 kDa-like toxin substrate 1 MAPT microtubule-associatedITPR2 inositol 1,4,5-protein tau triphosphate receptor, type 2 ALS2CR4amyotrophic lateral GLS glutaminase sclerosis 2 (juvenile) chromosomeregion, candidate 4 ALS2CR8 amyotrophic lateral CNTFR ciliaryneurotrophic factor sclerosis 2 (juvenile) receptor chromosome region,candidate 8 ALS2CR11 amyotrophic lateral FOLH1 folate hydrolase 1sclerosis 2 (juvenile) chromosome region, candidate 11 FAM117B familywith sequence P4HB prolyl 4-hydroxylase, similarity 117, member B betapolypeptide CNTF ciliary neurotrophic factor SQSTM1 sequestosome 1STRADB STE20-related kinase NAIP NLR family, apoptosis adaptor betainhibitory protein YWHAQ tyrosine 3-SLC33A1 solute carrier family 33monooxygenase/tryptoph (acetyl-CoA transporter), an 5-monooxygenasemember 1 activation protein, theta polypeptide TRAK2 traffickingprotein, FIG. 4 FIG. 4 homolog, SAC1 kinesin binding 2 lipid phosphatasedomain containing NIF3L1 NIF3 NGG1 interacting INA internexin neuronalfactor 3-like 1 intermediate filament protein, alpha PARD3B par-3partitioning COX8A cytochrome c oxidase defective 3 homolog B subunitVIIIA CDK15 cyclin-dependent kinase HECW1 HECT, C2 and WW 15 domaincontaining E3 ubiquitin protein ligase 1 NOS1 nitric oxide synthase 1MET met proto-oncogene SOD2 superoxide dismutase 2, HSPB1 heat shock 27kDa mitochondrial protein 1 NEFL neurofilament, light CTSB cathepsin Bpolypeptide ANG angiogenin, HSPA8 heat shock 70 kDa ribonuclease, RNaseA protein 8 family, 5 VAPB VAMP (vesicle-ESR1 estrogen receptor 1associated membrane protein)-associated protein B and C SNCA synuclein,alpha HGF hepatocyte growth factor CAT catalase ACTB actin, beta NEFMneurofilament, medium TH tyrosine hydroxylase polypeptide BCL2 B-cellCLL/lymphoma 2 FAS Fas (TNF receptor superfamily, member 6) CASP3caspase 3, apoptosis-CLU clusterin related cysteine peptidase SMN1survival of motor neuron G6PD glucose-6-phosphate 1, telomericdehydrogenase BAX BCL2-associated X HSF1 heat shock transcriptionprotein factor 1 RNF19A ring finger protein 19A JUN jun oncogeneALS2CR12 amyotrophic lateral HSPA5 heat shock 70 kDa sclerosis 2(juvenile) protein 5 chromosome region, candidate 12 MAPK14mitogen-activated protein IL10 interleukin 10 kinase 14 APEX1 APEXnuclease TXNRD1 thioredoxin reductase 1 (multifunctional DNA repairenzyme) 1 NOS2 nitric oxide synthase 2, TIMP1 TIMP metallopeptidaseinducible inhibitor 1 CASP9 caspase 9, apoptosis-XIAP X-linked inhibitorof related cysteine apoptosis peptidase GLG1 golgi glycoprotein 1 EPOerythropoietin VEGFA vascular endothelial ELN elastin growth factor AGDNF glial cell derived NFE2L2 nuclear factor (erythroid-neurotrophicfactor derived 2)-like 2 SLC6A3 solute carrier family 6 HSPA4 heat shock70 kDa (neurotransmitter protein 4 transporter, dopamine), member 3 APOEapolipoprotein E PSMB8 proteasome (prosome, macropain) subunit, betatype, 8 DCTN1 dynactin 1 TIMP3 TIMP metallopeptidase inhibitor 3 KIFAP3kinesin-associated SLC1A1 solute carrier family 1 protein 3(neuronal/epithelial high affinity glutamate transporter, system Xag),member 1 SMN2 survival of motor neuron CCNC cyclin C 2, centromeric MPP4membrane protein, STUB1 STIP1 homology and U-palmitoylated 4 boxcontaining protein 1 ALS2 amyloid beta (A4) PRDX6 peroxiredoxin 6precursor protein SYP synaptophysin CABIN1 calcineurin binding protein 1CASP1 caspase 1, apoptosis-GART phosphoribosylglycinami related cysteinede formyltransferase, peptidase phosphoribosylglycinami de synthetase,phosphoribosylaminoimidazole synthetase CDK5 cyclin-dependent kinase 5ATXN3 ataxin 3 RTN4 reticulon 4 C1QB complement component 1, qsubcomponent, B chain VEGFC nerve growth factor HTT huntingtin receptorPARK7 Parkinson disease 7 XDH xanthine dehydrogenase GFAP glialfibrillary acidic MAP2 microtubule-associated protein protein 2 CYCScytochrome c, somatic FCGR3B Fc fragment of IgG, low affinity IIIb, CCScopper chaperone for UBL5 ubiquitin-like 5 superoxide dismutase MMP9matrix metallopeptidase SLC18A3 solute carrier family 18 9 ((vesicularacetylcholine), member 3 TRPM7 transient receptor HSPB2 heat shock 27kDa potential cation channel, protein 2 subfamily M, member 7 AKT1 v-aktmurine thymoma DERL1 Der1-like domain family, viral oncogene homolog 1member 1 CCL2 chemokine (C-C motif) NGRN neugrin, neurite ligand 2outgrowth associated GSR glutathione reductase TPPP3 tubulinpolymerization-promoting protein family member 3 APAF1 apoptoticpeptidase BTBD10 BTB (POZ) domain activating factor 1 containing 10GLUD1 glutamate CXCR4 chemokine (C-X-C motif) dehydrogenase 1 receptor 4SLCIA3 solute carrier family 1 FLT1 fms-related tyrosine (glial highaffinity glutamate transporter), member 3 kinase 1 PON1 paraoxonase 1 ARandrogen receptor LIF leukemia inhibitory factor ERBB3 v-erb-b2erythroblastic leukemia viral oncogene homolog 3 LGALS1 lectin,galactoside-CD44 CD44 molecule binding, soluble, 1 TP53 tumor proteinp53 TLR3 toll-like receptor 3 GRIA1 glutamate receptor, GAPDHglyceraldehyde-3-ionotropic, AMPA 1 phosphate dehydrogenase GRIK1glutamate receptor, DES desmin ionotropic, kainate 1 CHAT cholineacetyltransferase FLT4 fins-related tyrosine kinase 4 CHMP2B chromatinmodifying BAG1 BCL2-associated protein 2B athanogene MT3 metallothionein3 CHRNA4 cholinergic receptor, nicotinic, alpha 4 GSS glutathionesynthetase BAK1 BCL2-antagonist/killer 1 KDR kinase insert domain GSTP1glutathione S-transferase receptor (a type III pi 1 receptor tyrosinekinase) OGG1 8-oxoguanine DNA IL6 interleukin 6 (interferon, glycosylasebeta 2).

The animal or cell may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or moredisrupted chromosomal sequences encoding a protein associated with ALSand zero, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more chromosomally integratedsequences encoding the disrupted protein associated with ALS. Preferredproteins associated with ALS include SOD1 (superoxide dismutase 1), ALS2(amyotrophic lateral sclerosis 2), FUS (fused in sarcoma), TARDBP (TARDNA binding protein), VAGFA (vascular endothelial growth factor A),VAGFB (vascular endothelial growth factor B), and VAGFC (vascularendothelial growth factor C), and any combination thereof.

Examples of proteins associated with prion diseases may include SOD1(superoxide dismutase 1), ALS2 (amyotrophic lateral sclerosis 2), FUS(fused in sarcoma), TARDBP (TAR DNA binding protein), VAGFA (vascularendothelial growth factor A), VAGFB (vascular endothelial growth factorB), and VAGFC (vascular endothelial growth factor C), and anycombination thereof.

Examples of proteins related to neurodegenerative conditions in priondisorders may include A2M (Alpha-2-Macroglobulin), AATF (Apoptosisantagonizing transcription factor), ACPP (Acid phosphatase prostate),ACTA2 (Actin alpha 2 smooth muscle aorta), ADAM22 (ADAM metallopeptidasedomain), ADORA3 (Adenosine A3 receptor), or ADRA1D (Alpha-1D adrenergicreceptor for Alpha-1D adrenoreceptor), for example.

Examples of proteins associated with Immunodeficiency may include A2M[alpha-2-macroglobulin]; AANAT [arylalkylamine N-acetyltransferase];ABCA1 [ATP-binding cassette, sub-family A (ABC1), member 1]; ABCA2[ATP-binding cassette, sub-family A (ABC1), member 2]; or ABCA3[ATP-binding cassette, sub-family A (ABC1), member 3]; for example.

Examples of proteins associated with Trinucleotide Repeat Disordersinclude AR (androgen receptor), FMR1 (fragile X mental retardation 1),HTT (huntingtin), or DMPK (dystrophia myotonica-protein kinase), FXN(frataxin), ATXN2 (ataxin 2), for example.

Examples of proteins associated with Neurotransmission Disorders includeSST (somatostatin), NOS1 (nitric oxide synthase 1 (neuronal)), ADRA2A(adrenergic, alpha-2A-, receptor), ADRA2C (adrenergic, alpha-2C-,receptor), TACR1 (tachykinin receptor 1), or HTR2c (5-hydroxytryptamine(serotonin) receptor 2C), for example.

Examples of neurodevelopmental-associated sequences include A2BP1[ataxin 2-binding protein 1], AADAT [aminoadipate aminotransferase],AANAT [arylalkylamine N-acetyltransferase], ABAT [4-aminobutyrateaminotransferase], ABCA1 [ATP-binding cassette, sub-family A (ABC1),member 1], or ABCA13 [ATP-binding cassette, sub-family A (ABC1), member13], for example.

Further examples of preferred conditions treatable with the presentsystem include may be selected from: Aicardi-Goutières Syndrome;Alexander Disease; Allan-Herndon-Dudley Syndrome; POLG-RelatedDisorders; Alpha-Mannosidosis (Type II and III); Alström Syndrome;Angelman; Syndrome; Ataxia-Telangiectasia; NeuronalCeroid-Lipofuscinoses; Beta-Thalassemia; Bilateral Optic Atrophy and(Infantile) Optic Atrophy Type 1; Retinoblastoma (bilateral); CanavanDisease; Cerebrooculofacioskeletal Syndrome 1 [COFS1]; CerebrotendinousXanthomatosis; Cornelia de Lange Syndrome; MAPT-Related Disorders;Genetic Prion Diseases; Dravet Syndrome; Early-Onset Familial AlzheimerDisease; Friedreich Ataxia [FRDA]; Fryns Syndrome; Fucosidosis; FukuyamaCongenital Muscular Dystrophy; Galactosialidosis; Gaucher Disease;Organic Acidemias; Hemophagocytic Lymphohistiocytosis;Hutchinson-Gilford Progeria Syndrome; Mucolipidosis II; Infantile FreeSialic Acid Storage Disease; PLA2G6-Associated Neurodegeneration;Jervell and Lange-Nielsen Syndrome; Junctional Epidermolysis Bullosa;Huntington Disease; Krabbe Disease (Infantile); MitochondrialDNA-Associated Leigh Syndrome and NARP; Lesch-Nyhan Syndrome;LIS1-Associated Lissencephaly; Lowe Syndrome; Maple Syrup Urine Disease;MECP2 Duplication Syndrome; ATP7A-Related Copper Transport Disorders:LAMA2-Related Muscular Dystrophy; Arylsulfatase A Deficiency;Mucopolysaccharidosis Types I, II or III; Peroxisome BiogenesisDisorders, Zellweger Syndrome Spectrum; Neurodegeneration with BrainIron Accumulation Disorders; Acid Sphingomyelinase Deficiency;Niemann-Pick Disease Type C; Glycine Encephalopathy; ARX-RelatedDisorders; Urea Cycle Disorders; COL1A1/2-Related OsteogenesisImperfecta; Mitochondrial DNA Deletion Syndromes; PLP1-RelatedDisorders; Perry Syndrome; Phelan-McDermid Syndrome; Glycogen StorageDisease Type II (Pompe Disease) (Infantile); MAPT-Related Disorders;MECP2-Related Disorders; Rhizomelic Chondrodysplasia Punctata Type 1;Roberts Syndrome; Sandhoff Disease; Schindler Disease—Type 1; AdenosineDeaminase Deficiency; Smith-Lemli-Opitz Syndrome; Spinal MuscularAtrophy; Infantile-Onset Spinocerebellar Ataxia; Hexosaminidase ADeficiency; Thanatophoric Dysplasia Type 1; Collagen Type VI-RelatedDisorders; Usher Syndrome Type I; Congenital Muscular Dystrophy;Wolf-Hirschhorn Syndrome; Lysosomal Acid Lipase Deficiency; andXeroderma Pigmentosum.

As will be apparent, it is envisaged that the present system can be usedto target any polynucleotide sequence of interest. Some examples ofconditions or diseases that might be usefully treated using the presentsystem are included in the Tables above and examples of genes currentlyassociated with those conditions are also provided there. However, thegenes exemplified are not exhaustive.

For example, “wild type StCas9” refers to wild type Cas9 from S.thermophilus, the protein sequence of which is given in the SwissProtdatabase under accession number G3ECR1. Similarly, S. pyogenes Cas9 isincluded in SwissProt under accession number Q99ZW2.

The ability to use CRISPR-Cas systems to perform efficient and costeffective gene editing and manipulation will allow the rapid selectionand comparison of single and multiplexed genetic manipulations totransform such genomes for improved production and enhanced traits. Inthis regard reference is made to US patents and publications: U.S. Pat.No. 6,603,061—Agrobacterium-Mediated Plant Transformation Method; U.S.Pat. No. 7,868,149-Plant Genome Sequences and Uses Thereof and US2009/0100536—Transgenic Plants with Enhanced Agronomic Traits, all thecontents and disclosure of each of which are herein incorporated byreference in their entirety. In the practice of the invention, thecontents and disclosure of Morrell et al “Crop genomics: advances andapplications” Nat Rev Genet. 2011 Dec. 29; 13(2):85-96 are also hereinincorporated by reference in their entirety.

EXAMPLES

The following examples are given for the purpose of illustrating variousembodiments of the invention and are not meant to limit the presentinvention in any fashion. The present examples, along with the methodsdescribed herein are presently representative of preferred embodiments,are exemplary, and are not intended as limitations on the scope of theinvention. Changes therein and other uses which are encompassed withinthe spirit of the invention as defined by the scope of the claims willoccur to those skilled in the art.

Example 1 CRISPR Complex Activity in the Nucleus of a Eukaryotic Cell

An example type II CRISPR system is the type II CRISPR locus fromStreptococcus pyogenes SF370, which contains a cluster of four genesCas9, Cas1, Cas2, and Csn1, as well as two non-coding RNA elements,tracrRNA and a characteristic array of repetitive sequences (directrepeats) interspaced by short stretches of non-repetitive sequences(spacers, about 30 bp each). In this system, targeted DNA double-strandbreak (DSB) is generated in four sequential steps (FIG. 2A). First, twonon-coding RNAs, the pre-crRNA array and tracrRNA, are transcribed fromthe CRISPR locus. Second, tracrRNA hybridizes to the direct repeats ofpre-crRNA, which is then processed into mature crRNAs containingindividual spacer sequences. Third, the mature crRNA:tracrRNA complexdirects Cas9 to the DNA target consisting of the protospacer and thecorresponding PAM via heteroduplex formation between the spacer regionof the crRNA and the protospacer DNA. Finally, Cas9 mediates cleavage oftarget DNA upstream of PAM to create a DSB within the protospacer (FIG.2A). This example describes an example process for adapting thisRNA-programmable nuclease system to direct CRISPR complex activity inthe nuclei of eukaryotic cells.

Cell Culture and Transfection

Human embryonic kidney (HEK) cell line HEK 293FT (Life Technologies) wasmaintained in Dulbecco's modified Eagle's Medium (DMEM) supplementedwith 10% fetal bovine serum (HyClone), 2 mM GlutaMAX (LifeTechnologies), 100 U/mL penicillin, and 100 μg/mL streptomycin at 37° C.with 5% CO₂ incubation. Mouse neuro2A (N2A) cell line (ATCC) wasmaintained with DMEM supplemented with 5% fetal bovine serum (HyClone),2 mM GlutaMAX (Life Technologies), 100 U/mL penicillin, and 100 μg/mLstreptomycin at 37° C. with 5% CO₂.

HEK 293FT or N2A cells were seeded into 24-well plates (Corning) one dayprior to transfection at a density of 200,000 cells per well. Cells weretransfected using Lipofectamine 2000 (Life Technologies) following themanufacturer's recommended protocol. For each well of a 24-well plate atotal of 800 ng of plasmids were used.

Surveyor Assay and Sequencing Analysis for Genome Modification

HEK 293FT or N2A cells were transfected with plasmid DNA as describedabove. After transfection, the cells were incubated at 37° C. for 72hours before genomic DNA extraction. Genomic DNA was extracted using theQuickExtract DNA extraction kit (Epicentre) following the manufacturer'sprotocol. Briefly, cells were resuspended in QuickExtract solution andincubated at 65° C. for 15 minutes and 98° C. for 10 minutes. Extractedgenomic DNA was immediately processed or stored at −20° C.

The genomic region surrounding a CRISPR target site for each gene wasPCR amplified, and products were purified using QiaQuick Spin Column(Qiagen) following manufacturer's protocol. A total of 400 ng of thepurified PCR products were mixed with 2 μl 10× Taq polymerase PCR buffer(Enzymatics) and ultrapure water to a final volume of 20 μl, andsubjected to a re-annealing process to enable heteroduplex formation:95° C. for 10 min, 95° C. to 85° C. ramping at −2° C./s, 85° C. to 25°C. at −0.25° C./s, and 25° C. hold for 1 minute. After re-annealing,products were treated with Surveyor nuclease and Surveyor enhancer S(Transgenomics) following the manufacturer's recommended protocol, andanalyzed on 4-20% Novex TBE poly-acrylamide gels (Life Technologies).Gels were stained with SYBR Gold DNA stain (Life Technologies) for 30minutes and imaged with a Gel Doc gel imaging system (Bio-rad).Quantification was based on relative band intensities, as a measure ofthe fraction of cleaved DNA. FIG. 7 provides a schematic illustration ofthis Surveyor assay.

Restriction fragment length polymorphism assay for detection ofhomologous recombination.

HEK 293FT and N2A cells were transfected with plasmid DNA, and incubatedat 37° C. for 72 hours before genomic DNA extraction as described above.The target genomic region was PCR amplified using primers outside thehomology arms of the homologous recombination (HR) template. PCRproducts were separated on a 1% agarose gel and extracted with MinEluteGelExtraction Kit (Qiagen). Purified products were digested with HindIII(Fermentas) and analyzed on a 6% Novex TBE poly-acrylamide gel (LifeTechnologies).

RNA Secondary Structure Prediction and Analysis

RNA secondary structure prediction was performed using the onlinewebserver RNAfold developed at Institute for Theoretical Chemistry atthe University of Vienna, using the centroid structure predictionalgorithm (see e.g. A. R. Gruber et al., 2008, Cell 106(1): 23-24; and PA Carr and G M Church, 2009, Nature Biotechnology 27(12): 1151-62).

RNA Purification

HEK 293FT cells were maintained and transfected as stated above. Cellswere harvested by trypsinization followed by washing in phosphatebuffered saline (PBS). Total cell RNA was extracted with TRI reagent(Sigma) following manufacturer's protocol. Extracted total RNA wasquantified using Naonodrop (Thermo Scientific) and normalized to sameconcentration.

Northern Blot Analysis of crRNA and tracrRNA Expression in MammalianCells

RNAs were mixed with equal volumes of 2× loading buffer (Ambion), heatedto 95° C. for 5 min, chilled on ice for 1 min, and then loaded onto 8%denaturing polyacrylamide gels (SequaGel, National Diagnostics) afterpre-running the gel for at least 30 minutes. The samples wereelectrophoresed for 1.5 hours at 40 W limit. Afterwards, the RNA wastransferred to Hybond N+ membrane (GE Healthcare) at 300 mA in asemi-dry transfer apparatus (Bio-rad) at room temperature for 1.5 hours.The RNA was crosslinked to the membrane using autocrosslink button onStratagene UV Crosslinker the Stratalinker (Stratagene). The membranewas pre-hybridized in ULTRAhyb-Oligo Hybridization Buffer (Ambion) for30 min with rotation at 42° C., and probes were then added andhybridized overnight. Probes were ordered from IDT and labeled with[gamma-³²P] ATP (Perkin Elmer) with T4 polynucleotide kinase (NewEngland Biolabs). The membrane was washed once with pre-warmed (42° C.)2×SSC, 0.5% SDS for 1 min followed by two 30 minute washes at 42° C. Themembrane was exposed to a phosphor screen for one hour or overnight atroom temperature and then scanned with a phosphorimager (Typhoon).

Bacterial CRISPR System Construction and Evaluation

CRISPR locus elements, including tracrRNA, Cas9, and leader were PCRamplified from Streptococcus pyogenes SF370 genomic DNA with flankinghomology arms for Gibson Assembly. Two BsaI type IIS sites wereintroduced in between two direct repeats to facilitate easy insertion ofspacers (FIG. 8). PCR products were cloned into EcoRV-digested pACYC184downstream of the tet promoter using Gibson Assembly Master Mix (NEB).Other endogenous CRISPR system elements were omitted, with the exceptionof the last 50 bp of Csn2. Oligos (Integrated DNA Technology) encodingspacers with complimentary overhangs were cloned into the BsaI-digestedvector pDC000 (NEB) and then ligated with T7 ligase (Enzymatics) togenerate pCRISPR plasmids. Challenge plasmids containing spacers withPAM

expression in mammalian cells (expression constructs illustrated in FIG.6A, with functionality as determined by results of the Surveyor assayshown in FIG. 6B). Transcription start sites are marked as +1, andtranscription terminator and the sequence probed by northern blot arealso indicated. Expression of processed tracrRNA was also confirmed byNorthern blot. FIG. 6C shows results of a Northern blot analysis oftotal RNA extracted from 293FT cells transfected with U6 expressionconstructs carrying long or short tracrRNA, as well as SpCas9 andDR-EMX1(1)-DR. Left and right panels are from 293FT cells transfectedwithout or with SpRNase III, respectively. U6 indicate loading controlblotted with a probe targeting human U6 snRNA. Transfection of the shorttracrRNA expression construct led to abundant levels of the processedform of tracrRNA (˜75 bp). Very low amounts of long tracrRNA aredetected on the Northern blot.

To promote precise transcriptional initiation, the RNA polymeraseIII-based U6 promoter was selected to drive the expression of tracrRNA(FIG. 2C). Similarly, a U6 promoter-based construct was developed toexpress a pre-crRNA array consisting of a single spacer flanked by twodirect repeats (DRs, also encompassed by the term “tracr-matesequences”; FIG. 2C). The initial spacer was designed to target a33-base-pair (bp) target site (30-bp protospacer plus a 3-bp CRISPRmotif (PAM) sequence satisfying the NGG recognition motif of Cas9) inthe human EMX1 locus (FIG. 2C), a key gene in the development of thecerebral cortex.

To test whether heterologous expression of the CRISPR system (SpCas9,SpRNase III, tracrRNA, and pre-crRNA) in mammalian cells can achievetargeted cleavage of mammalian chromosomes, HEK 293FT cells weretransfected with combinations of CRISPR components. Since DSBs inmammalian nuclei are partially repaired by the non-homologous endjoining (NHEJ) pathway, which leads to the formation of indels, theSurveyor assay was used to detect potential cleavage activity at thetarget EMX1 locus (FIG. 7) (see e.g. Guschin et al., 2010, Methods MolBiol 649: 247). Co-transfection of all four CRISPR components was ableto induce up to 5.0% cleavage in the protospacer (see FIG. 2D).Co-transfection of all CRISPR components minus SpRNase III also inducedup to 4.7% indel in the protospacer, suggesting that there may beendogenous mammalian RNases that are capable of assisting with crRNAmaturation, such as for example the related Dicer and Drosha enzymes.Removing any of the remaining three components abolished the genomecleavage activity of the CRISPR system (FIG. 2D). Sanger sequencing ofamplicons containing the target locus verified the cleavage activity: in43 sequenced clones, 5 mutated alleles (11.6%) were found. Similarexperiments using a variety of guide sequences produced indelpercentages as high as 29% (see FIGS. 3-6, 10, and 11). These resultsdefine a three-component system for efficient CRISPR-mediated genomemodification in mammalian cells. To optimize the cleavage efficiency,Applicants also tested whether different isoforms of tracrRNA affectedthe cleavage efficiency and found that, in this example system, only theshort (89-bp) transcript form was able to mediate cleavage of the humanEMX1 genomic locus (FIG. 6B).

FIG. 12 provides an additional Northern blot analysis of crRNAprocessing in mammalian cells. FIG. 12A illustrates a schematic showingthe expression vector for a single spacer flanked by two direct repeats(DR-EMX1(1)-DR). The 30 bp spacer targeting the human EMX1 locusprotospacer 1 (see FIG. 6) and the direct repeat sequences are shown inthe sequence beneath FIG. 12A. The line indicates the region whosereverse-complement sequence was used to generate Northern blot probesfor EMX1(1) crRNA detection. FIG. 12B shows a Northern blot analysis oftotal RNA extracted from 293FT cells transfected with U6 expressionconstructs carrying DR-EMX1(1)-DR. Left and right panels are from 293FTcells transfected without or with SpRNase III respectively.DR-EMX1(1)-DR was processed into mature crRNAs only in the presence ofSpCas9 and short tracrRNA and was not dependent on the presence ofSpRNase III. The mature crRNA detected from transfected 293FT total RNAis −33 bp and is shorter than the 39-42 bp mature crRNA from S.pyogenes. These results demonstrate that a CRISPR system can betransplanted into eukaryotic cells and reprogrammed to facilitatecleavage of endogenous mammalian target polynucleotides.

FIG. 2 illustrates the bacterial CRISPR system described in thisexample. FIG. 2A illustrates a schematic showing the CRISPR locus 1 fromStreptococcus pyogenes SF370 and a proposed mechanism of CRISPR-mediatedDNA cleavage by this system. Mature crRNA processed from the directrepeat-spacer array directs Cas9 to genomic targets consisting ofcomplimentary protospacers and a protospacer-adjacent motif (PAM). Upontarget-spacer base pairing, Cas9 mediates a double-strand break in thetarget DNA. FIG. 2B illustrates engineering of S. pyogenes Cas9 (SpCas9)and RNase III (SpRNase III) with nuclear localization signals (NLSs) toenable import into the mammalian nucleus. FIG. 2C illustrates mammalianexpression of SpCas9 and SpRNase III driven by the constitutive EF1apromoter and tracrRNA and pre-crRNA array (DR-Spacer-DR) driven by theRNA Pol3 promoter U6 to promote precise transcription initiation andtermination. A protospacer from the human EMX1 locus with a satisfactoryPAM sequence is used as the spacer in the pre-crRNA array. FIG. 2Dillustrates surveyor nuclease assay for SpCas9-mediated minor insertionsand deletions. SpCas9 was expressed with and without SpRNase III,tracrRNA, and a pre-crRNA array carrying the EMX1-target spacer. FIG. 2Eillustrates a schematic representation of base pairing between targetlocus and EMX1-targeting crRNA, as well as an example chromatogramshowing a micro deletion adjacent to the SpCas9 cleavage site. FIG. 2Fillustrates mutated alleles identified from sequencing analysis of 43clonal amplicons showing a variety of micro insertions and deletions.Dashes indicate deleted bases, and non-aligned or mismatched basesindicate insertions or mutations. Scale bar=10 μm.

To further simplify the three-component system, a chimericcrRNA-tracrRNA hybrid design was adapted, where a mature crRNA(comprising a guide sequence) may be fused to a partial tracrRNA via astem-loop to mimic the natural crRNA:tracrRNA duplex. To increaseco-delivery efficiency, a bicistronic expression vector was created todrive co-expression of a chimeric RNA and SpCas9 in transfected cells.In parallel, the bicistronic vectors were used to express a pre-crRNA(DR-guide sequence-DR) with SpCas9, to induce processing into crRNA witha separately expressed tracrRNA (compare FIG. 11B top and bottom). FIG.8 provides schematic illustrations of bicistronic expression vectors forpre-crRNA array (FIG. 8A) or chimeric crRNA (represented by the shortline downstream of the guide sequence insertion site and upstream of theEF1α promoter in FIG. 8B) with hSpCas9, showing location of variouselements and the point of guide sequence insertion. The expandedsequence around the location of the guide sequence insertion site inFIG. 8B also shows a partial DR sequence (GTTTAGAGCTA) and a partialtracrRNA sequence (TAGCAAGTTAAAATAAGGCTAGTCCGTTTTT). Guide sequences canbe inserted between BbsI sites using annealed oligonucleotides. Sequencedesign for the oligonucleotides are shown below the schematicillustrations in FIG. 8, with appropriate ligation adapters indicated.WPRE represents the Woodchuck hepatitis virus post-transcriptionalregulatory element. The efficiency of chimeric RNA-mediated cleavage wastested by targeting the same EMX1 locus described above. Using bothSurveyor assay and Sanger sequencing of amplicons, Applicants confirmedthat the chimeric RNA design facilitates cleavage of human EMX1 locuswith approximately a 4.7% modification rate (FIG. 3).

Generalizability of CRISPR-mediated cleavage in eukaryotic cells wastested by targeting additional genomic loci in both human and mousecells by designing chimeric RNA targeting multiple sites in the humanEMX1 and PVALB, as well as the mouse Th loci. FIG. 13 illustrates theselection of some additional targeted protospacers in human PVALB (FIG.13A) and mouse Th (FIG. 13B) loci. Schematics of the gene loci and thelocation of three protospacers within the last exon of each areprovided. The underlined sequences include 30 bp of protospacer sequenceand 3 bp at the 3′ end corresponding to the PAM sequences. Protospacerson the sense and anti-sense strands are indicated above and below theDNA sequences, respectively. A modification rate of 6.3% and 0.75% wasachieved for the human PVALB and mouse Th loci respectively,demonstrating the broad applicability of the CRISPR system in modifyingdifferent loci across multiple organisms (FIG. 5). While cleavage wasonly detected with one out of three spacers for each locus using thechimeric constructs, all target sequences were cleaved with efficiencyof indel production reaching 27% when using the co-expressed pre-crRNAarrangement (FIGS. 6 and 13).

FIG. 11 provides a further illustration that SpCas9 can be reprogrammedto target multiple genomic loci in mammalian cells. FIG. 11A provides aschematic of the human EMX1 locus showing the location of fiveprotospacers, indicated by the underlined sequences. FIG. 11B provides aschematic of the pre-crRNA/trcrRNA complex showing hybridization betweenthe direct repeat region of the pre-crRNA and tracrRNA (top), and aschematic of a chimeric RNA design comprising a 20 bp guide sequence,and tracr mate and tracr sequences consisting of partial direct repeatand tracrRNA sequences hybridized in a hairpin structure (bottom).Results of a Surveyor assay comparing the efficacy of Cas9-mediatedcleavage at five protospacers in the human EMX1 locus is illustrated inFIG. 11C. Each protospacer is targeted using either processedpre-crRNA/tracrRNA complex (crRNA) or chimeric RNA (chiRNA).

Since the secondary structure of RNA can be crucial for intermolecularinteractions, a structure prediction algorithm based on minimum freeenergy and Boltzmann-weighted structure ensemble was used to compare theputative secondary structure of all guide sequences used in the genometargeting experiment (see e.g. Gruber et al., 2008, Nucleic AcidsResearch, 36: W70). Analysis revealed that in most cases, the effectiveguide sequences in the chimeric crRNA context were substantially free ofsecondary structure motifs, whereas the ineffective guide sequences weremore likely to form internal secondary structures that could preventbase pairing with the target protospacer DNA. It is thus possible thatvariability in the spacer secondary structure might impact theefficiency of CRISPR-mediated interference when using a chimeric crRNA.

Further vector designs for SpCas9 are shown in FIG. 22, whichillustrates single expression vectors incorporating a U6 promoter linkedto an insertion site for a guide oligo, and a Cbh promoter linked toSpCas9 coding sequence. The vector shown in FIG. 22 b includes atracrRNA coding sequence linked to an H1 promoter.

In the bacterial assay, all spacers facilitated efficient CRISPRinterference (FIG. 3C). These results suggest that there may beadditional factors affecting the efficiency of CRISPR activity inmammalian cells.

To investigate the specificity of CRISPR-mediated cleavage, the effectof single-nucleotide mutations in the guide sequence on protospacercleavage in the mammalian genome was analyzed using a series ofEMX1-targeting chimeric crRNAs with single point mutations (FIG. 3A).FIG. 3B illustrates results of a Surveyor nuclease assay comparing thecleavage efficiency of Cas9 when paired with different mutant chimericRNAs. Single-base mismatch up to 12-bp 5′ of the PAM substantiallyabrogated genomic cleavage by SpCas9, whereas spacers with mutations atfarther upstream positions retained activity against the originalprotospacer target (FIG. 3B). In addition to the PAM, SpCas9 hassingle-base specificity within the last 12-bp of the spacer.Furthermore, CRISPR is able to mediate genomic cleavage as efficientlyas a pair of TALE nucleases (TALEN) targeting the same EMX1 protospacer.FIG. 3C provides a schematic showing the design of TALENs targetingEMX1, and FIG. 3D shows a Surveyor gel comparing the efficiency of TALENand Cas9 (n=3).

Having established a set of components for achieving CRISPR-mediatedgene editing in mammalian cells through the error-prone NHEJ mechanism,the ability of CRISPR to stimulate homologous recombination (HR), a highfidelity gene repair pathway for making precise edits in the genome, wastested. The wild type SpCas9 is able to mediate site-specific DSBs,which can be repaired through both NHEJ and HR. In addition, anaspartate-to-alanine substitution (D10A) in the RuvC I catalytic domainof SpCas9 was engineered to convert the nuclease into a nickase(SpCas9n; illustrated in FIG. 4A) (see e.g. Sapranausaks et al., 2011,Nucleic Acids Resch, 39: 9275; Gasiunas et al., 2012, Proc. Natl. Acad.Sci. USA, 109:E2579), such that nicked genomic DNA undergoes thehigh-fidelity homology-directed repair (HDR). Surveyor assay confirmedthat SpCas9n does not generate indels at the EMX1 protospacer target. Asillustrated in FIG. 4B, co-expression of EMX1-targeting chimeric crRNAwith SpCas9 produced indels in the target site, whereas co-expressionwith SpCas9n did not (n=3). Moreover, sequencing of 327 amplicons didnot detect any indels induced by SpCas9n. The same locus was selected totest CRISPR-mediated HR by co-transfecting HEK 293FT cells with thechimeric RNA targeting EMX1, hSpCas9 or hSpCas9n, as well as a HRtemplate to introduce a pair of restriction sites (HindIII and NheI)near the protospacer. FIG. 4C provides a schematic illustration of theHR strategy, with relative locations of recombination points and primerannealing sequences (arrows). SpCas9 and SpCas9n indeed catalyzedintegration of the HR template into the EMX1 locus. PCR amplification ofthe target region followed by restriction digest with HindIII revealedcleavage products corresponding to expected fragment sizes (arrows inrestriction fragment length polymorphism gel analysis shown in FIG. 4D),with SpCas9 and SpCas9n mediating similar levels of HR efficiencies.Applicants further verified HR using Sanger sequencing of genomicamplicons (FIG. 4E). These results demonstrate the utility of CRISPR forfacilitating targeted gene insertion in the mammalian genome. Given the14-bp (12-bp from the spacer and 2-bp from the PAM) target specificityof the wild type SpCas9, the availability of a nickase can significantlyreduce the likelihood of off-target modifications, since single strandbreaks are not substrates for the error-prone NHEJ pathway.

Expression constructs mimicking the natural architecture of CRISPR lociwith arrayed spacers (FIG. 2A) were constructed to test the possibilityof multiplexed sequence targeting. Using a single CRISPR array encodinga pair of EMX1- and PVALB-targeting spacers, efficient cleavage at bothloci was detected (FIG. 4F, showing both a schematic design of the crRNAarray and a Surveyor blot showing efficient mediation of cleavage).Targeted deletion of larger genomic regions through concurrent DSBsusing spacers against two targets within EMX1 spaced by 119 bp was alsotested, and a 1.6% deletion efficacy (3 out of 182 amplicons; FIG. 4G)was detected. This demonstrates that the CRISPR system can mediatemultiplexed editing within a single genome.

Example 2 CRISPR System Modifications and Alternatives

The ability to use RNA to program sequence-specific DNA cleavage definesa new class of genome engineering tools for a variety of research andindustrial applications. Several aspects of the CRISPR system can befurther improved to increase the efficiency and versatility of CRISPRtargeting. Optimal Cas9 activity may depend on the availability of freeMg²⁺ at levels higher than that present in the mammalian nucleus (seee.g. Jinek et al., 2012, Science, 337:816), and the preference for anNGG motif immediately downstream of the protospacer restricts theability to target on average every 12-bp in the human genome (FIG. 9,evaluating both plus and minus strands of human chromosomal sequences).Some of these constraints can be overcome by exploring the diversity ofCRISPR loci across the microbial metagenome (see e.g. Makarova et al.,2011, Nat Rev Microbiol, 9:467). Other CRISPR loci may be transplantedinto the mammalian cellular milieu by a process similar to thatdescribed in Example 1. For example, FIG. 10 illustrates adaptation ofthe Type II CRISPR system from CRISPR 1 of Streptococcus thermophilusLMD-9 for heterologous expression in mammalian cells to achieveCRISPR-mediated genome editing. FIG. 10A provides a Schematicillustration of CRISPR 1 from S. thermophilus LMD-9. FIG. 10Billustrates the design of an expression system for the S. thermophilusCRISPR system. Human codon-optimized hStCas9 is expressed using aconstitutive EF1α promoter. Mature versions of tracrRNA and crRNA areexpressed using the U6 promoter to promote precise transcriptioninitiation. Sequences from the mature crRNA and tracrRNA areillustrated. A single base indicated by the lower case “a” in the crRNAsequence is used to remove the polyU sequence, which serves as a RNApolIII transcriptional terminator. FIG. 10C provides a schematic showingguide sequences targeting the human EMX1 locus. FIG. 10D shows theresults of hStCas9-mediated cleavage in the target locus using theSurveyor assay. RNA guide spacers 1 and 2 induced 14% and 6.4%,respectively. Statistical analysis of cleavage activity acrossbiological replica at these two protospacer sites is also provided inFIG. 5. FIG. 14 provides a schematic of additional protospacer andcorresponding PAM sequence targets of the S. thermophilus CRISPR systemin the human EMX1 locus. Two protospacer sequences are highlighted andtheir corresponding PAM sequences satisfying NNAGAAW motif are indicatedby underlining 3′ with respect to the corresponding highlightedsequence. Both protospacers target the anti-sense strand.

Example 3 Sample Target Sequence Selection Algorithm

A software program is designed to identify candidate CRISPR targetsequences on both strands of an input DNA sequence based on desiredguide sequence length and a CRISPR motif sequence (PAM) for a specifiedCRISPR enzyme. For example, target sites for Cas9 from S. pyogenes, withPAM sequences NGG, may be identified by searching for 5′-N_(x)-NGG-3′both on the input sequence and on the reverse-complement of the input.Likewise, target sites for Cas9 of S. thermophilus CRISPR1, with PAMsequence NNAGAAW, may be identified by searching for 5′-N_(x)-NNAGAAW-3′both on the input sequence and on the reverse-complement of the input.Likewise, target sites for Cas9 of S. thermophilus CRISPR3, with PAMsequence NGGNG, may be identified by searching for 5′-N_(x)-NGGNG-3′both on the input sequence and on the reverse-complement of the input.The value “x” in N_(x) may be fixed by the program or specified by theuser, such as 20.

Since multiple occurrences in the genome of the DNA target site may leadto nonspecific genome editing, after identifying all potential sites,the program filters out sequences based on the number of times theyappear in the relevant reference genome. For those CRISPR enzymes forwhich sequence specificity is determined by a ‘seed’ sequence, such asthe 11-12 bp 5′ from the PAM sequence, including the PAM sequenceitself, the filtering step may be based on the seed sequence. Thus, toavoid editing at additional genomic loci, results are filtered based onthe number of occurrences of the seed:PAM sequence in the relevantgenome. The user may be allowed to choose the length of the seedsequence. The user may also be allowed to specify the number ofoccurrences of the seed:PAM sequence in a genome for purposes of passingthe filter. The default is to screen for unique sequences. Filtrationlevel is altered by changing both the length of the seed sequence andthe number of occurrences of the sequence in the genome. The program mayin addition or alternatively provide the sequence of a guide sequencecomplementary to the reported target sequence(s) by providing thereverse complement of the identified target sequence(s). An examplevisualization of some target sites in the human genome is provided inFIG. 18.

Further details of methods and algorithms to optimize sequence selectioncan be found in U.S. application Ser. No. 61/064,798 (Attorney docket44790.11.2022; Broad Reference BI-2012/084); incorporated herein byreference.

Example 4 Evaluation of Multiple Chimeric crRNA-tracrRNA Hybrids

This example describes results obtained for chimeric RNAs (chiRNAs;comprising a guide sequence, a tracr mate sequence, and a tracr sequencein a single transcript) having tracr sequences that incorporatedifferent lengths of wild-type tracrRNA sequence. FIG. 16 a illustratesa schematic of a bicistronic expression vector for chimeric RNA andCas9. Cas9 is driven by the CBh promoter and the chimeric RNA is drivenby a U6 promoter. The chimeric guide RNA consists of a 20 bp guidesequence (Ns) joined to the tracr sequence (running from the first “U”of the lower strand to the end of the transcript), which is truncated atvarious positions as indicated. The guide and tracr sequences areseparated by the tracr-mate sequence GUUUUAGAGCUA followed by the loopsequence GAAA. Results of SURVEYOR assays for Cas9-mediated indels atthe human EMX1 and PVALB loci are illustrated in FIGS. 16 b and 16 c,respectively. Arrows indicate the expected SURVEYOR fragments. ChiRNAsare indicated by their “+n” designation, and crRNA refers to a hybridRNA where guide and tracr sequences are expressed as separatetranscripts. Quantification of these results, performed in triplicate,are illustrated by histogram in FIGS. 17 a and 17 b, corresponding toFIGS. 16 b and 16 c, respectively (“N.D.” indicates no indels detected).Protospacer IDs and their corresponding genomic target, protospacersequence, PAM sequence, and strand location are provided in Table D.Guide sequences were designed to be complementary to the entireprotospacer sequence in the case of separate transcripts in the hybridsystem, or only to the underlined portion in the case of chimeric RNAs.

TABLE D protospacer genomic ID target protospacer sequence (5′ to 3′) PAM strand 1 EMX1 GGACATCGATGTCACCTCCAATGACTAGCG TGG + 2 EMX1CATTGGAGGTGACATCGATGTCCTCCCCAT TGG − 3 EMX1GGAAGGGCCTGAGTCCGAGCAGAAGAAGAA GGG + 4 PVALBGGTGGCGAGAGGGGCCGAGATTGGGTGTTC AGG + 5 PVALBATGCAGGAGGGTGGCGAGAGGGGCCGAGAT TGG +

Further details to optimize guide sequences can be found in U.S.application Ser. No. 61/836,127 (Attorney docket 44790.08.2022; BroadReference BI-2013/004G); incorporated herein by reference.

Initially, three sites within the EMX1 locus in human HEK 293FT cellswere targeted. Genome modification efficiency of each chiRNA wasassessed using the SURVEYOR nuclease assay, which detects mutationsresulting from DNA double-strand breaks (DSBs) and their subsequentrepair by the non-homologous end joining (NHEJ) DNA damage repairpathway. Constructs designated chiRNA(+n) indicate that up to the +nnucleotide of wild-type tracrRNA is included in the chimeric RNAconstruct, with values of 48, 54, 67, and 85 used for n. Chimeric RNAscontaining longer fragments of wild-type tracrRNA (chiRNA(+67) andchiRNA(+85)) mediated DNA cleavage at all three EMX1 target sites, withchiRNA(+85) in particular demonstrating significantly higher levels ofDNA cleavage than the corresponding crRNA/tracrRNA hybrids thatexpressed guide and tracr sequences in separate transcripts (FIGS. 16 band 17 a). Two sites in the PVALB locus that yielded no detectablecleavage using the hybrid system (guide sequence and tracr sequenceexpressed as separate transcripts) were also targeted using chiRNAs.chiRNA(+67) and chiRNA(+85) were able to mediate significant cleavage atthe two PVALB protospacers (FIGS. 16 c and 17 b).

For all five targets in the EMX1 and PVALB loci, a consistent increasein genome modification efficiency with increasing tracr sequence lengthwas observed. Without wishing to be bound by any theory, the secondarystructure formed by the 3′ end of the tracrRNA may play a role inenhancing the rate of CRISPR complex formation.

Example 5 Cas9 Diversity

The CRISPR-Cas system is an adaptive immune mechanism against invadingexogenous DNA employed by diverse species across bacteria and archaea.The type II CRISPR-Cas9 system consists of a set of genes encodingproteins responsible for the “acquisition” of foreign DNA into theCRISPR locus, as well as a set of genes encoding the “execution” of theDNA cleavage mechanism; these include the DNA nuclease (Cas9), anon-coding transactivating cr-RNA (tracrRNA), and an array of foreignDNA-derived spacers flanked by direct repeats (crRNAs). Upon maturationby Cas9, the tracRNA and crRNA duplex guide the Cas9 nuclease to atarget DNA sequence specified by the spacer guide sequences, andmediates double-stranded breaks in the DNA near a short sequence motifin the target DNA that is required for cleavage and specific to eachCRISPR-Cas system. The type II CRISPR-Cas systems are found throughoutthe bacterial kingdom and highly diverse in in Cas9 protein sequence andsize, tracrRNA and crRNA direct repeat sequence, genome organization ofthese elements, and the motif requirement for target cleavage. Onespecies may have multiple distinct CRISPR-Cas systems.

Applicants evaluated 207 putative Cas9s from bacterial speciesidentified based on sequence homology to known Cas9s and structuresorthologous to known subdomains, including the HNH endonuclease domainand the RuvC endonuclease domains [information from the Eugene Kooninand Kira Makarova]. Phylogenetic analysis based on the protein sequenceconservation of this set revealed five families of Cas9s, includingthree groups of large Cas9s (˜1400 amino acids) and two of small Cas9s(˜1100 amino acids) (see FIGS. 19 and 20A-F).

Further details of Cas9s and mutations of the Cas9 enzyme to convertinto a nickase or DNA binding protein and use of same with alteredfunctionality can be found in U.S. application Ser. Nos. 61/836,101 and61/835,936 (Attorney docket 44790.09.2022 and 4790.07.2022 and BroadReference BI-2013/004E and BI-2013/004F respectively) incorporatedherein by reference.

Example 6 Cas9 Orthologs

Applicants analyzed Cas9 orthologs to identify the relevant PAMsequences and the corresponding chimeric guide RNA. Having an expandedset of PAMs provides broader targeting across the genome and alsosignificantly increases the number of unique target sites and providespotential for identifying novel Cas9s with increased levels ofspecificity in the genome.

The specificity of Cas9 orthologs can be evaluated by testing theability of each Cas9 to tolerate mismatches between the guide RNA andits DNA target. For example, the specificity of SpCas9 has beencharacterized by testing the effect of mutations in the guide RNA oncleavage efficiency. Libraries of guide RNAs were made with single ormultiple mismatches between the guide sequence and the target DNA. Basedon these findings, target sites for SpCas9 can be selected based on thefollowing guidelines:

To maximize SpCas9 specificity for editing a particular gene, one shouldchoose a target site within the locus of interest such that potential‘off-target’ genomic sequences abide by the following four constraints:First and foremost, they should not be followed by a PAM with either5′-NGG or NAG sequences. Second, their global sequence similarity to thetarget sequence should be minimized. Third, a maximal number ofmismatches should lie within the PAM-proximal region of the off-targetsite. Finally, a maximal number of mismatches should be consecutive orspaced less than four bases apart.

Similar methods can be used to evaluate the specificity of other Cas9orthologs and to establish criteria for the selection of specific targetsites within the genomes of target species. As mentioned previouslyphylogenetic analysis based on the protein sequence conservation of thisset revealed five families of Cas9s, including three groups of largeCas9s (˜1400 amino acids) and two of small Cas9s (˜1100 amino acids)(see FIGS. 19 and 20A-F). Further details on Cas orthologs can be foundin U.S. application Ser. Nos. 61/836,101 and 61/835,936 (Attorney docket44790.09.2022 and 4790.07.2022 and Broad Reference BI-2013/004E andBI-2013/004F respectively) incorporated herein by reference.

Example 7 Methodological Improvement to Simplify Cloning and Delivery

Rather than encoding the U6-promoter and guide RNA on a plasmid,Applicants amplified the U6 promoter with a DNA oligo to add on theguide RNA. The resulting PCR product may be transfected into cells todrive expression of the guide RNA.

Example primer pair that allows the generation a PCR product consistingof U6-promoter::guideRNA targeting human Emx1 locus:

Forward Primer: AAACTCTAGAgagggcctatttcccatgattc

Reverse Primer (carrying the guide RNA, which is underlined):

acctctagAAAAAAAGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCATTTTAACTTGCTATGCCTTTGTTTTGTTTCCAAAACAGCATAGCTCTAAAACCCCTAGTCATTGGAGGTGACG GTGTTTCGTCCTTTCCACaag

Example 8 Methodological Improvement to Improve Activity

Rather than use pol3 promoters, in particular RNA polymerase III (e.g.U6 or H1 promoters), to express guide RNAs in eukaryotic cells,Applicants express the T7 polymerase in eukaryotic cells to driveexpression of guide RNAs using the T7 promoter.

One example of this system may involve introduction of three pieces ofDNA:

1. expression vector for Cas9

2. expression vector for T7 polymerase

3. expression vector containing guideRNA fused to the T7 promoter

Example 9 Methodological Improvement to Reduce Toxicity of Cas9:Delivery of Cas9 in the Form of mRNA

Delivery of Cas9 in the form of mRNA enables transient expression ofCas9 in cells, to reduce toxicity. For example, humanized SpCas9 may beamplified using the following primer pair:

Forward Primer (to add on T7 promoter for in vitro transcription):

TAATACGACTCACTATAGGAAGTGCGCCACCATGGC CCCAAAGAAGAAGCGG

Reverse Primer (to add on polyA tail):

GGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTttcttaCT TTTTCTTTTTTGCCTGGCCG 

Applicants transfect the Cas9 mRNA into cells with either guide RNA inthe form of RNA or DNA cassettes to drive guide RNA expression ineukaryotic cells.

Example 10 Methodological Improvement to Reduce Toxicity of Cas9: Use ofan Inducible Promoter

Applicants transiently turn on Cas9 expression only when it is neededfor carrying out genome modification. Examples of inducible systeminclude tetracycline inducible promoters (Tet-On or Tet-Off), smallmolecule two-hybrid transcription activations systems (FKBP, ABA, etc),or light inducible systems (Phytochrome, LOV domains, or cryptochrome).

Example 11 Improvement of the Cas9 System for In Vivo Application

Applicants conducted a Metagenomic search for a Cas9 with smallmolecular weight. Most Cas9 homologs are fairly large. For example theSpCas9 is around 1368aa long, which is too large to be easily packagedinto viral vectors for delivery. A graph representing the lengthdistribution of Cas9 homologs is generated from sequences deposited inGenBank (FIG. 23). Some of the sequences may have been mis-annotated andtherefore the exact frequency for each length may not necessarily beaccurate. Nevertheless it provides a glimpse at distribution of Cas9proteins and suggest that there are shorter Cas9 homologs.

Through computational analysis, Applicants found that in the bacterialstrain Campylobacter, there are two Cas9 proteins with less than 1000amino acids. The sequence for one Cas9 from Campylobacter jejuni ispresented below. At this length, CjCas9 can be easily packaged into AAV,lentiviruses, Adenoviruses, and other viral vectors for robust deliveryinto primary cells and in vivo in animal models. In a preferredembodiment of the invention, the Cas9 protein from S. aureus is used.

>Campylobacter jejuni Cas9 (CjCas9)MARILAFDIGISSIGWAFSENDELKDCGVRIFTKVENPKTGESLALPRRLARSARKRLARRKARLNHLKHLIANEFKLNYEDYQSFDESLAKAYKGSLISPYELRFRALNELLSKQDFARVILHIAKRRGYDDIKNSDDKEKGMLKAIKQNEEKLANYQSVGEYLYKEYFQKFKENSKEFTNVRNKKESYERCIAQSFLKDELKIAFKKQREFGFSFSKKFEEEVLSVAFYKRALKDFSHINGNCSFFTDEKRAPKNSPLAFMFVALTRIINLINNLKNTEGILYTKDDLNALLNEVLKNGTUFYKQTKKLLGLSDDYEFKGEKGTYHEFKKYKEFIKALGEHNLSQDDLNEIAKDITLIKDEIKLKKALAKYDLNQNQIDSLSKLEFKUHLNISFKALKLNTPLMLEGKKYDEACNELNLKVAIINEDKKDFLPAFNETYYKDEVTNPVVLRAIIKEYRKVLNALLKKYGKVMINIEIAREVGKNFISQRAKIEKEQNENYKAKKDAELECEKLGLKINSKNILKLRLFKEQKEFCAYSGEKIKISDLQDEKMLEIDHIYPYSRSFDDSYMNKVINFTKQNQEKLNQTPFEAFGNDSAKWQKIEVLAKNLPTKKQKRILDKNYKDKEQKNFKDRNLNDTRYIARLVLNYTKDYLDFITLSDDENTKLNDTQKGSKVHVEAKSCIMLTSALRHTWGFSAICDRNNHLHHAIDAVIIAYANNSIVKAFSDFKKEQESNSAELYAKKISTLDYKNKRKFTEPFSGERQKVIDKIDEIFVSKPERKKPSCIALFIEETFRKEEEFYQSYGGKEGVLKALELGKIRKVNGKIVKNGDMFRVDIFKEIKKTNKFYAVPIYTMDFALKVLPNKAVARSKKGEIKDWILMDENYEFCFSLYKDSLILIQTKDMQEPEFVYYNAFTSSTVSLIVSKIADNKFETLSKNQKILFKNANEKEVIAKSIGIQNLKVFEKYWSALGEVTKAEFRQREDFKK

The putative tracrRNA element for this CjCas9 is:

TATAATCTCATAAGAAATTTAAAAAGGGACTAAAATAAAGAGTTTGCGGGACTCTGCGGGGTTACAATCCCCTAAAACCGCTTTTAAAATT

The Direct Repeat sequence is:

ATTTTACCATAAAGAAATTTAAAAAGGGACTAAAAC

An example of a chimeric guideRNA for CjCas9 is:

NNNNNNNNNNNNNNNNNNNNGUUUUAGUCCCGAAAGGGACUAAAAUAAAGAGUUUGCGGGACUCUGCGGGGUUACAAUCCCCUAAAACCGCU UUU

Example 12 Cas9 Optimization

For enhanced function or to develop new functions, Applicants generatechimeric Cas9 proteins by combining fragments from different Cas9homologs. For example, two example chimeric Cas9 proteins:

For example, Applicants fused the N-term of St1Cas9 (fragment from thisprotein is in bold) with C-term of SpCas9 (fragment from this protein isunderlined).

>St1(N)Sp(C)Cas9 MSDLVLGLDIGIGSVGVGIILNKVTGEHHKNSRIFPAAQAENNLVRRTNRQGRRLARRKKHRRVRLNRLFEESGLITDVIKISINLNPYQLRVKGLIDELSNEELHALKNININKTIRGISYLDDASDDGNSSVGDYAQIWKENSKQLETKTPGIMLERYQTYGQLRGDFTVEKDGKKHRLINVFPTSAYRSEALRILQTQQEFNPQITDEHNRYLEILTGKRKYYHGPGNEKSRTDYGRYRTSGETLDNIFGILIGKCTFYPDEFRAAKASYTAQEFNLLNDLNNLTVPTETKKLSKEQKNQIINYVKNEKAMGPAKLFKYIAKILLSCDVADIKGYRIDKSGKAMITFEAYRKMKTILETLDIEQMDRETIDKLAYNTLTLNTEREGIQEALEHEFADGSFSQKQVDELVQFRKANSSIFGKGWHNFSVKLMMEIWELYETSKEQMTELTRILGKQKTTSSSNKTKYIDEKLLTEEIYNPVVAKSVROAIKIVINAAIKEYGDFDNIVIEMARE NQTTQKGOKNSRERNIKRIEEGINKELGSQILKEHPVETQLIONEKINLYYLQNGRDMYVDQELDINRISDYDVDIIIVPQSFIXDDSIDNKVILTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKEIVAQIIDSMNTKIDENDKLIREVKVITIKSKINSDRKDIFQFYKYREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFICTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVMVKKTEVQTGGFSKESILPKRINSDKIIARKKDWDPKKYGGFDSPTVAYSVINVAKVEKGKSICKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSIFELENGRKRMILASAGELQKGNEALPSKYVNFLYLASIIYEKLKGSPEDNEQKQLEVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIFIQSITGLYETRIDLSQLGGD >Sp(N)St1(C)Cas9MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKITIQINQTYNQUEENPINASGVDAKAIISARISKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLOLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEETKAPLSASMIKRYDEHFIQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKYKYVTEGMRKRAFLSGFKKAIVDLIFKTNRKVINKKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQUHDDSEKEDIQKAQVSGQGDSUIEFTIANLAGSPAIKKGILQTVKVVDEINKVMGRHK PENIVIEMARETNEDDEKKMQMQKANKDEKDAAMLKAANQYNGKAELPHSVFHGHKQLATKIRLWHQQGERCLYTGKTISIHDLINNSNQFEVDHILPLSITFDDSLANKVINYATANQEKGQRTPWALDSMDDAWSFRELKAFVRESKTLSNKKKENLLTEEDISKHARKKFIERNLVDTRYASIZVVLNALQERFRARKIDTKVSVVRGQFTSQLRRHWGIEKTRIYIYHHHAVDALIINASSQLNLWKKQKNTLVSYSEDQLLLDIETGELISDDEYKESVFKAPYQHFVDTLKSKEFEDSILFSYQVDSKFNRKISDATIYATRQAKVGKDKADETYYLGKIKDIYTQDGYDAFMKIYKKDKSKFLMYRHDPQTFEKVIEFILENYPNKQINEKGKEVPCNPFLKYKEEHIGYIRKYSKKGNGPEIKSLKYYDSKLGNIIIDFIPIKDSNNKVAILQSVSPWRADVYFNKTTGKYEILGLKYADLQFEKGTCTYKISQEKYNDIKKKEGVDSDSEFKFTLYKNDLLLVKDTETKEQQLFRFLSRTMPKQKHYVELKPYDKQKFEGGEALIKVLGNVANSGQCKKGLCKSNISIYIKVRTDVLGNQIIIIKNEGDKPKLDF

The benefit of making chimeric Cas9 include:

reduce toxicity

improve expression in eukaryotic cells

enhance specificity

reduce molecular weight of protein, make protein smaller by combiningthe smallest domains from different Cas9 homologs.

Altering the PAM sequence requirement

Example 13 Utilization of Cas9 as a Generic DNA Binding Protein

Applicants used Cas9 as a generic DNA binding protein by mutating thetwo catalytic domains (D10 and H840) responsible for cleaving bothstrands of the DNA target. In order to upregulate gene transcription ata target locus Applicants fused the transcriptional activation domain(VP64) to Cas9. Applicants hypothesized that it would be important tosee strong nuclear localization of the Cas9-VP64 fusion protein becausetranscription factor activation strength is a function of time spent atthe target. Therefore, Applicants cloned a set of Cas9-VP64-GFPconstructs, transfected them into 293 cells and assessed theirlocalization under a fluorescent microscope 12 hours post-transfection.

The same constructs were cloned as a 2A-GFP rather than a direct fusionin order to functionally test the constructs without a bulky GFP presentto interfere. Applicants elected to target the Sox2 locus with the Cas9transactivator because it could be useful for cellular reprogram and thelocus has already been validated as a target for TALE-TF mediatedtranscriptional activation. For the Sox2 locus Applicants chose eighttargets near the transcriptional start site (TSS). Each target was 20 bplong with a neighboring NGG protospacer adjacent motif (PAM). EachCas9-VP64 construct was co-transfected with each PCR generated chimericcrispr RNA (chiRNA) in 293 cells. 72 hours post transfection thetranscriptional activation was assessed using RT-qPCR.

To further optimize the transcriptional activator, Applicants titratedthe ratio of chiRNA (Sox2.1 and Sox2.5) to Cas9(NLS-VP64-NLS-hSpCas9-NLS-VP64-NLS), transfected into 293 cells, andquantified using RT-qPCR. These results indicate that Cas9 can be usedas a generic DNA binding domain to upregulate gene transcription at atarget locus.

Applicants designed a second generation of constructs. (Table below).

pLenti-EF1a-GFP-2A-6xHis-NLS-VP64-NLS-hSpCsn1(D10A, H840A)-NLSpLenti-EF1a-GFP-2A-6xHis-NLS-VP64-NLS-hSpCsn1(D10A, H840A)pLenti-EF1a-GFP-2A-6xHis-NLS-VP64-NLS-NLS-hSpCsn1(D10A, H840A)pLenti-EF1a-GFP-2A-6xHis-NLS-hSpCsn1(D10A, H840A)-NLSpLenti-EF1a-GFP-2A-6xHis-NLS-hSpCsn1(D10A, H840A)pLenti-EF1a-GFP-2A-6xHis-NLS-NLS-hSpCsn1(D10A, H840A)

Applicants use these constructs to assess transcriptional activation(VP64 fused constructs) and repression (Cas9 only) by RT-qPCR.Applicants assess the cellular localization of each construct usinganti-His antibody, nuclease activity using a Surveyor nuclease assay,and DNA binding affinity using a gel shift assay. In a preferredembodiment of the invention, the gel shift assay is an EMSA gel shiftassay.

Example 14 Cas9 Transgenic and Knock in Mice

To generate a mouse that expresses the Cas9 nuclease Applicants submittwo general strategies, transgenic and knock in. These strategies may beapplied to generate any other model organism of interest, for e.g. Rat.For each of the general strategies Applicants made a constitutivelyactive Cas9 and a Cas9 that is conditionally expressed (Cre recombinasedependent). The constitutively active Cas9 nuclease is expressed in thefollowing context: pCAG-NLS-Cas9-NLS-P2A-EGFP-WPRE-bGHpolyA. pCAG is thepromoter, NLS is a nuclear localization signal, P2A is the peptidecleavage sequence, EGFP is enhanced green fluorescent protein, WPRE isthe woodchuck hepatitis virus posttranscriptional regulatory element,and bGHpolyA is the bovine growth hormone poly-A signal sequence (FIGS.25A-B). The conditional version has one additional stop cassetteelement, loxP-SV40 polyA x3-loxP, after the promoter and beforeNLS-Cas9-NLS (i.e.pCAG-loxP-SV40polyAx3-loxP-NLS-Cas9-NLS-P2A-EGFP-WPRE-bGHpolyA). Theimportant expression elements can be visualized as in FIG. 26. Theconstitutive construct should be expressed in all cell types throughoutdevelopment, whereas, the conditional construct will only allow Cas9expression when the same cell is expressing the Cre recombinase. Thislatter version will allow for tissue specific expression of Cas9 whenCre is under the expression of a tissue specific promoter. Moreover,Cas9 expression could be induced in adult mice by putting Cre under theexpression of an inducible promoter such as the TET on or off system.

Validation of Cas9 constructs: Each plasmid was functionally validatedin three ways: 1) transient transfection in 293 cells followed byconfirmation of GFP expression; 2) transient transfection in 293 cellsfollowed by immunofluorescence using an antibody recognizing the P2Asequence; and 3) transient transfection followed by Surveyor nucleaseassay. The 293 cells may be 293FT or 293 T cells depending on the cellsthat are of interest. In a preferred embodiment the cells are 293FTcells. The results of the Surveyor were run out on the top and bottomrow of the gel for the conditional and constitutive constructs,respectively. Each was tested in the presence and absence of chimericRNA targeted to the hEMX1 locus (chimeric RNA hEMX1.1). The resultsindicate that the construct can successfully target the hEMX1 locus onlyin the presence of chimeric RNA (and Cre in the conditional case). Thegel was quantified and the results are presented as average cuttingefficiency and standard deviation for three samples.

Transgenic Cas9 mouse: To generate transgenic mice with constructs,Applicants inject pure, linear DNA into the pronucleus of a zygote froma pseudo pregnant CB56 female. Founders are identified, genotyped, andbackcrossed to CB57 mice. The constructs were successfully cloned andverified by Sanger sequencing.

Knock in Cas9 mouse: To generate Cas9 knock in mice Applicants targetthe same constitutive and conditional constructs to the Rosa26 locus.Applicants did this by cloning each into a Rosa26 targeting vector withthe following elements: Rosa26 short homologyarm—constitutive/conditional Cas9 expression cassette—pPGK-Neo-Rosa26long homology arm—pPGK-DTA. pPGK is the promoter for the positiveselection marker Neo, which confers resistance to neomycin, a 1 kb shortarm, a 4.3 kb long arm, and a negative selection diphtheria toxin (DTA)driven by PGK.

The two constructs were electroporated into R1 mESCs and allowed to growfor 2 days before neomycin selection was applied. Individual coloniesthat had survived by days 5-7 were picked and grown in individual wells.5-7 days later the colonies were harvested, half were frozen and theother half were used for genotyping. Genotyping was done by genomic PCR,where one primer annealed within the donor plasmid (AttpF) and the otheroutside of the short homology arm (Rosa26-R) Of the 22 coloniesharvested for the conditional case, 7 were positive (Left). Of the 27colonies harvested for the constitutive case, zero were positive(Right). It is likely that Cas9 causes some level of toxicity in themESC and for this reason there were no positive clones. To test thisApplicants introduced a Cre expression plasmid into correctly targetedconditional Cas9 cells and found very low toxicity after many days inculture. The reduced copy number of Cas9 in correctly targetedconditional Cas9 cells (1-2 copies per cell) is enough to allow stableexpression and relatively no cytotoxicity. Moreover, this data indicatesthat the Cas9 copy number determines toxicity. After electroporationeach cell should get several copies of Cas9 and this is likely why nopositive colonies were found in the case of the constitutive Cas9construct. This provides strong evidence that utilizing a conditional,Cre-dependent strategy should show reduced toxicity. Applicants injectcorrectly targeted cells into a blastocyst and implant into a femalemouse. Chimerics are identified and backcrossed. Founders are identifiedand genotyped.

Utility of the conditional Cas9 mouse: Applicants have shown in 293cells that the Cas9 conditional expression construct can be activated byco-expression with Cre. Applicants also show that the correctly targetedR1 mESCs can have active Cas9 when Cre is expressed. Because Cas9 isfollowed by the P2A peptide cleavage sequence and then EGFP Applicantsidentify successful expression by observing EGFP. This same concept iswhat makes the conditional Cas9 mouse so useful. Applicants may crosstheir conditional Cas9 mouse with a mouse that ubiquitously expressesCre (ACTB-Cre line) and may arrive at a mouse that expresses Cas9 inevery cell. It should only take the delivery of chimeric RNA to inducegenome editing in embryonic or adult mice. Interestingly, if theconditional Cas9 mouse is crossed with a mouse expressing Cre under atissue specific promoter, there should only be Cas9 in the tissues thatalso express Cre. This approach may be used to edit the genome in onlyprecise tissues by delivering chimeric RNA to the same tissue.

Example 15 Cas9 Diversity and Chimeric RNAs

The CRISPR-Cas system is an adaptive immune mechanism against invadingexogenous DNA employed by diverse species across bacteria and archaea.The type II CRISPR-Cas system consists of a set of genes encodingproteins responsible for the “acquisition” of foreign DNA into theCRISPR locus, as well as a set of genes encoding the “execution” of theDNA cleavage mechanism; these include the DNA nuclease (Cas9), anon-coding transactivating cr-RNA (tracrRNA), and an array of foreignDNA-derived spacers flanked by direct repeats (crRNAs). Upon maturationby Cas9, the tracrRNA and crRNA duplex guide the Cas9 nuclease to atarget DNA sequence specified by the spacer guide sequences, andmediates double-stranded breaks in the DNA near a short sequence motifin the target DNA that is required for cleavage and specific to eachCRISPR-Cas system. The type II CRISPR-Cas systems are found throughoutthe bacterial kingdom and highly diverse in in Cas9 protein sequence andsize, tracrRNA and crRNA direct repeat sequence, genome organization ofthese elements, and the motif requirement for target cleavage. Onespecies may have multiple distinct CRISPR-Cas systems.

Applicants evaluated 207 putative Cas9s from bacterial speciesidentified based on sequence homology to known Cas9s and structuresorthologous to known subdomains, including the HNH endonuclease domainand the RuvC endonuclease domains [information from the Eugene Kooninand Kira Makarova]. Phylogenetic analysis based on the protein sequenceconservation of this set revealed five families of Cas9s, includingthree groups of large Cas9s (˜1400 amino acids) and two of small Cas9s(˜1100 amino acids) (FIGS. 19A-D and 20A-F).

Applicants have also optimized Cas9 guide RNA using in vitro methods.

Example 16 Cas9 Mutations

In this example, Applicants show that the following mutations canconvert SpCas9 into a nicking enzyme: D10A, E762A, H840A, N854A, N863A,D986A.

Applicants provide sequences showing where the mutation points arelocated within the SpCas9 gene (FIG. 24A-M). Applicants also show thatthe nickases are still able to mediate homologous recombination.Furthermore, Applicants show that SpCas9 with these mutations(individually) do not induce double strand break.

Cas9 orthologs all share the general organization of 3-4 RuvC domainsand a HNH domain. The 5′ most RuvC domain cleaves the non-complementarystrand, and the HNH domain cleaves the complementary strand. Allnotations are in reference to the guide sequence.

The catalytic residue in the 5′ RuvC domain is identified throughhomology comparison of the Cas9 of interest with other Cas9 orthologs(from S. pyogenes type II CRISPR locus, S. thermophilus CRISPR locus 1,S. thermophilus CRISPR locus 3, and Franciscilla novicida type II CRISPRlocus), and the conserved Asp residue is mutated to alanine to convertCas9 into a complementary-strand nicking enzyme. Similarly, theconserved His and Asn residues in the HNH domains are mutated to Alanineto convert Cas9 into a non-complementary-strand nicking enzyme.

Example 17 Cas9 Transcriptional Activation and Cas9 Repressor

Cas9 Transcriptional Activation

A second generation of constructs were designed and tested (Table 1).These constructs are used to assess transcriptional activation (VP64fused constructs) and repression (Cas9 only) by RT-qPCR. Applicantsassess the cellular localization of each construct using anti-H isantibody, nuclease activity using a Surveyor nuclease assay, and DNAbinding affinity using a gel shift assay.

Cas Repressor

It has been shown previously that dCas9 can be used as a generic DNAbinding domain to repress gene expression. Applicants report an improveddCas9 design as well as dCas9 fusions to the repressor domains KRAB andSID4x. From the plasmid library created for modulating transcriptionusing Cas9 in Table 1, the following repressor plasmids werefunctionally characterized by qPCR: pXRP27, pXRP28, pXRP29, pXRP48,pXRP49, pXRP50, pXRP51, pXRP52, pXRP53, pXRP56, pXRP58, pXRP59, pXRP61,and pXRP62.

Each dCas9 repressor plasmid was co-transfected with two guide RNAstargeted to the coding strand of the beta-catenin gene. RNA was isolated72 hours after transfection and gene expression was quantified byRT-qPCR. The endogenous control gene was GAPDH. Two validated shRNAswere used as positive controls. Negative controls were certain plasmidstransfected without gRNA, these are denoted as “pXRP## control”. Theplasmids pXRP28, pXRP29, pXRP48, and pXRP49 could repress thebeta-catenin gene when using the specified targeting strategy. Theseplasmids correspond to dCas9 without a functional domain (pXRP28 andpXRP28) and dCas9 fused to SID4x (pXRP48 and pXRP49).

Further work investigates: repeating the above experiment, targetingdifferent genes, utilizing other gRNAs to determine the optimaltargeting position, and multiplexed repression.

TABLE 1pXRP024-pLenti2-EF1a-VP64-NLS-FLAG-Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP025-pLenti2-EF1a-VP64-NLS-GGGGS₃Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP026-pLenti2-EF1a-VP64-NLS-EAAAK₃Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP027-pLenti2-EF1a-NLS-FLAG-Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP028-pLenti2-EF1a-NLS-GGGGS₃Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP029-pLenti2-EF1a-NLS-EAAAK₃Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP030-pLenti2-pSV40-VP64-NLS-FLAG-Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP031-pLenti2-pPGK-VP64-NLS-FLAG-Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP032-pLenti2-LTR-VP64-NLS-FLAG-Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP033-pLenti2-pSV40-VP64-NLS-GGGGS₃Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP034-pLenti2-pPGK-VP64-NLS-GGGGS₃Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP035-pLenti2-LTR-VP64-NLS-GGGGS₃Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP036-pLenti2-pSV40-VP64-NLS-EAAAK₃Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP037-pLenti2-pPGK-VP64-NLS-EAAAK₃Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP038-pLenti2-LTR-VP64-NLS-EAAAK₃Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP048-pLenti2-EF1a-SID4x-NLS-FLAG-Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP049-pLenti2-EF1a-SID4X-NLS-GGGGS₃Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP050-pLenti2-EF1a-SID4X-NLS-EAAAK₃Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP051-pLenti2-EF1a-KRAR-NLS-FLAG-Liniker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP052-pLenti2-EF1a-KRAB-NLS-GGGGS₃Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP053-pLenti2-EF1a-KRAB-NLS-EAAAK₃Linker-dCas9-NLS-gLuc-2A-GFP-WPREpXRP054-pLenti2-EF1a-dCas9-Liniker-FLAG-NLS-VP64-gLuc-2A-GFP-WPREpXRP055-pLenti2-EF1a-dCas9-Linker-FLAG-NLS-SID4X-gLuc-2A-GFP-WPREpXRP056-pLenti2-EF1a-dCas9-Linker-FLAG-NLS-KRAB-gLuc-2A-GFP-WPREpXRP057-pLenti2-EF1a-dCas9-GGGGGS₃-NLS-VP64-gLuc-2A-GFP-WPREpXRP058-pLenti2-EF1a-dCas9-GGGGGS₃-NLS-SID4X-gLuc-2A-GFP-WPREpXRP059-pLenti2-EF1a-dCas9-GGGGGS₃-NLS-KRAB-gLuc-2A-GFP-WPREpXRP060-pLenti2-EF1a-dCas9-EAAAK₃-NLS-VP64-gLuc-2A-GFP-WPREpXRP061-pLenti2-EF1a-dCas9-EAAAK₃-NLS-SID4X-gLuc-2A-GFP-WPREpXRP062-pLenti2-EF1a-dCas9-EAAAK₃-NLS-KRAB-gLuc-2A-GFP-WPREpXRP024-pLenti2-EF1a-VP64-NLS-FLAG-Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP025-pLenti2-EF1a-VP64-NLS-GGGGS₃Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP026-pLenti2-EF1a-VP64-NLS-EAAAK₃Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP027-pLenti2-EF1a-NLS-FLAG-Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP028-pLenti2-EF1a-NLS-GGGGS₃Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP029-pLenti2-EF1a-NLS-EAAAK₃Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP030-pLenti2-pSV40-VP64-NLS-FLAG-Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP031-pLenti2-pPGK-VP64-NLS-FLAG-Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP032-pLenti2-ETR-VP64-NLS-FLAG-Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP033-pLenti2-pSV40-VP64-NLS-GGGGS₃Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP034-pLenti2-pPGK-VP64-NLS-GGGGS₃Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP035-pLenti2-LTR-VP64-NLS-GUGGS₃Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP036-pLenti2-pSV40-VP64-NLS-EAAAK₃Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP037-pLenti2-pPGK-VP64-NLS-EAAAK₃Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP038-pLenti2-LTR-VP64-NLS-EAAAK₃Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP048-pLenti2-EF1a-SID4x-NLS-FEAG-Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP049-pLenti2-EF1a-SID4X-NLS-GGGGS₃Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP050-pLenti2-EF1a-SID4X-NLS-EAAAK₃Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP051-pLenti2-EF1a-KRAB-NLS-FLAG-Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP052-pLenti2-EF1a-KRAB-NLS-GGGGS₃Linker-Cas9-NLS-gLuc-2A-GEP-WPREpXRP053-pLenti2-FF1a-KRAB-NLS-EAAAK₃Linker-Cas9-NLS-gLuc-2A-GFP-WPREpXRP054-pLenti2-EF1a-Cas9-Linker-FLAG-NLS-VP64-gLuc-2A-GFP-WPREpXRP055-pLenti2-EF1a-Cas9-Linker-FLAG-NLS-SID4X-gLuc-2A-GFP-WPREpXRP056-pLenti2-EF1a-Cas9-Linker-FLAG-NLS-KRAB-gLuc-2A-GFP-WPREpXRP057-pLenti2-EF1a-Cas9-GGGGGS₃-NLS-VP64-gLuc-2A-GFP-WPREpXRP058-pLenti2-EF1a-Cas9-GGGGGS₃-NLS-SID4X-gLuc-2A-GFP-WPREpXRP059-pLenti2-EF1a-Cas9-GGGGGS₃-NLS-KRAB-gLuc-2A-GFP-WPREpXRP060-pLenti2-FF1a-Cas9-EAAAK₃-NES-VP64-gLuc-2A-GFP-WPREpXRP061-pLenti2-EF1a-Cas9-EAAAK₃-NES-SID4X-gLuc-2A-GFP-WPREpXRP062-pLenti2-EF1a-Cas9-EAAAK₃-NES-KRAB-gLuc-2A-GFP-WPRE

Example 18 Targeted Deletion of Genes Involved in CholesterolBiosynthesis, Fatty Acid Biosynthesis, and Other Metabolic Disorders,Genes Encoding Mis-Folded Proteins Involved in Amyloid and OtherDiseases, Oncogenes Leading to Cellular Transformation, Latent ViralGenes, and Genes Leading to Dominant-Negative Disorders, Amongst OtherDisorders

Applicants demonstrate gene delivery of a CRISPR-Cas system in theliver, brain, ocular, epithelial, hematopoetic, or another tissue of asubject or a patient in need thereof, suffering from metabolicdisorders, amyloidosis and protein-aggregation related diseases,cellular transformation arising from genetic mutations andtranslocations, dominant negative effects of gene mutations, latentviral infections, and other related symptoms, using either viral ornanoparticle delivery system.

Study Design:

Subjects or patients in need thereof suffering from metabolic disorders,amyloidosis and protein aggregation related disease which include butare not limited to human, non-primate human, canine, feline, bovine,equine, other domestic animals and related mammals. The CRISPR-Cassystem is guided by a chimeric guide RNA and targets a specific site ofthe human genomic loci to be cleaved. After cleavage and non-homologousend-joining mediated repair, frame-shift mutation results in knock outof genes.

Applicants select guide-RNAs targeting genes involved in above-mentioneddisorders to be specific to endogenous loci with minimal off-targetactivity. Two or more guide RNAs may be encoded into a single CRISPRarray to induce simultaneous double-stranded breaks in DNA leading tomicro-deletions of affected genes or chromosomal regions.

Identification and Design of Gene Targets

For each candidate disease gene, Applicants select DNA sequences ofinterest include protein-coding exons, sequences including and flankingknown dominant negative mutation sites, sequences including and flankingpathological repetitive sequences. For gene-knockout approaches, earlycoding exons closest to the start codon offer best options for achievingcomplete knockout and minimize possibility of truncated protein productsretaining partial function.

Applicants analyze sequences of interest for all possible targetable20-bp sequences immediately 5′ to a NGG motif (for SpCas9 system) or aNNAGAAW (for St1Cas9 system). Applicants choose sequences for unique,single RNA-guided Cas9 recognition in the genome to minimize off-targeteffects based on computational algorithm to determine specificity.

Cloning of Guide Sequences into a Delivery System

Guide sequences are synthesized as double-stranded 20-24 bpoligonucleotides. After 5′-phosphorylation treatment of oligos andannealing to form duplexes, oligos are ligated into suitable vectordepending on the delivery method:

Virus-Based Delivery Methods

AAV-based vectors (PX260, 330, 334, 335) have been described elsewhere

Lentiviral-based vectors use a similar cloning strategy of directlyligating guide sequences into a single vector carrying a U6promoter-driven chimeric RNA scaffold and a EF1a promoter-driven Cas9 orCas9 nickase.

Virus production is described elsewhere.

Nanoparticle-Based RNA Delivery Methods

1. Guide sequences are synthesized as an oligonucleotide duplex encodingT7 promoter-guide sequence-chimeric RNA. A T7 promoter is added 5′ ofCas9 by PCR method.

2. T7-driven Cas9 and guide-chimeric RNAs are transcribed in vitro, andCas9 mRNA is further capped and A-tailed using commercial kits. RNAproducts are purified per kit instructions.

Hydrodynamic Tail Vein Delivery Methods (for Mouse)

Guide sequences are cloned into AAV plasmids as described above andelsewhere in this application.

In Vitro Validation on Cell Lines

Transfection

1. DNA Plasmid Transfection

Plasmids carrying guide sequences are transfected into human embryonickidney (HEK293T) or human embryonic stem (hES) cells, other relevantcell types using lipid-, chemical-, or electroporation-based methods.For a 24-well transfection of HEK293T cells (˜260,000 cells), 500 ng oftotal DNA is transfected into each single well using Lipofectamine 2000.For a 12-well transfection of hES cells, 1 ug of total DNA istransfected into a single well using Fugene HD.

2. RNA Transfection

Purified RNA described above is used for transfection into HEK293Tcells. 1-2 ug of RNA may be transfected into ˜260,000 usingLipofectamine 2000 per manufacturer's instruction. RNA delivery of Cas9and chimeric RNA is shown in FIG. 28.

Assay of Indel Formation In Vitro

Cells are harvested 72-hours post-transfection and assayed for indelformation as an indication of double-stranded breaks.

Briefly, genomic region around target sequence is PCR amplified(˜400-600 bp amplicon size) using high-fidelity polymerase. Products arepurified, normalized to equal concentration, and slowly annealed from95° C. to 4° C. to allow formation of DNA heteroduplexes. Postannealing, the Cel-I enzyme is used to cleave heteroduplexes, andresulting products are separated on a polyacrylamide gel and indelefficiency calculated.

In Vivo Proof of Principle in Animal

Delivery Mechanisms

AAV or Lentivirus production is described elsewhere.

Nanoparticle Formulation: RNA Mixed into Nanoparticle Formulation

Hydrodynamic tail vein injections with DNA plasmids in mice areconducted using a commercial kit

Cas9 and guide sequences are delivered as virus, nanoparticle-coated RNAmixture, or DNA plasmids, and injected into subject animals. A parallelset of control animals is injected with sterile saline, Cas9 and GFP, orguide sequence and GFP alone.

Three weeks after injection, animals are tested for amelioration ofsymptoms and sacrificed. Relevant organ systems analyzed for indelformation. Phenotypic assays include blood levels of HDL, LDL, lipids,

Assay for Indel Formation

DNA is extracted from tissue using commercial kits; indel assay will beperformed as described for in vitro demonstration.

Therapeutic applications of the CRISPR-Cas system are amenable forachieving tissue-specific and temporally controlled targeted deletion ofcandidate disease genes. Examples include genes involved in cholesteroland fatty acid metabolism, amyloid diseases, dominant negative diseases,latent viral infections, among other disorders.

Examples of a single guide-RNA to introduce targeted indels at a genelocus

Disease GENE SPACER PAM Mechanism References Hypercholes- HMG- GCCAAATTGCGG Knockout Fluvastatin: a review of its terolemia CR GACGACCCTpharmacology and use in the CG management ofhypercholesterolaemia.(Plosker GL et al. Drugs 1996, 51(3): 433-459)Hypercholes- SQLE CGAGGAGAC TGG Knockout Potential role of nonstatinterolemia CCCCGTTTC cholesterol lowering agents GG(Trapani et al. IUBMB Life, Volume 63, Issue 11, pages 964-971, November 2011) Hyperlipid- DGAT1 CCCGCCGCC AGG KnockoutDGAT1 inhibitors as anti-obesity emia GCCGTGGCTand anti-diabetic agents. (Birch CG AM et al. Current Opinion inDrug Discovery & Development Leukemia BCR- TGAGCTCTA AGG KnockoutKilling of leukemic cells with a ABL CGAGATCCABCR/ABL fusion gene by RNA CA interference (RNAi.).( Fuchs et al.Oncogene 2002, 21(37): 5716-5724)

Examples of a pair of guide-RNA to introduce chromosomal microdeletionat a gene locus

Disease GENE SPACER PAM Mechanism References Hyperlipid- PLIN2 CTCAAAATTTGG Micro- Perilipin-2 Null Mice are emia guide1 CATACCGGT deletionProtected Against Diet-Induced TG Obesity, Adipose InflammationHyperlipid- PLIN2 CGTTAAACA TGG Micro- and Fatty Liver Disease emiaguide2 ACAACCGGA deletion (McManaman JL et al. The CTJournal of Lipid Research, jlr.M035063. First Published onFeb. 12, 2013) Hyperlipid- SREBP TTCACCCCCG ggg Micro-Inhibition of SREBP by a Small emia guide1 CGGCGCTGA deletionMolecule, Betulin, Improves AT Hyperlipidemia and Insulin Hyperlipid-SREBP ACCACTACC agg Micro- Resistance and Reduces emia guide2 AGTCCGTCCdeletion Atherosclerotic Plaques (Tang J et AC al. Cell Metabolism, Volume 13, issue 1, 44-56, 5 Jan. 2011)

Example 19 Targeted Integration of Repair for Genes CarryingDisease-Causing Mutations; Reconstitution of Enzyme Deficiencies andOther Related Diseases

Study Design

I. Identification and Design of Gene Targets

-   -   Described in Example 22

II. Cloning of Guide Sequences and Repair Templates into a DeliverySystem

-   -   Described above in Example 22    -   Applicants clone DNA repair templates to include homology arms        with diseased allele as well a wild-type repair template

III. In Vitro Validation on Cell Lines

-   -   a. Transfection is described above in Example 22; Cas9, guide        RNAs, and repair template are co-transfected into relevant cell        types.    -   b. Assay for repair in vitro        -   i. Applicants harvest cells 72-hours post-transfection and            assay for repair        -   ii. Briefly, Applicants amplify genomic region around repair            template PCR using high-fidelity polymerase. Applicants            sequence products for decreased incidence of mutant allele.

IV. In Vivo Proof of Principle in Animal

-   -   a. Delivery mechanisms are described above Examples 22 and 34.    -   b. Assay for repair in vivo        -   i. Applicants perform the repair assay as described in the            in vitro demonstration.

V. Therapeutic Applications

-   -   The CRISPR-Cas system is amenable for achieving tissue-specific        and temporally controlled targeted deletion of candidate disease        genes. Examples include genes involved in cholesterol and fatty        acid metabolism, amyloid diseases, dominant negative diseases,        latent viral infections, among other disorders.

Example of one single missense mutation with repair template:

Disease GENE SPACER PAM Mechanism Reference Familial TTR AGCCTTTCTGA CGGV30M Transthyretin mutations in health amyloid ACACATGCA repairand disease (Joao et al. Human Mutation, polyneuropathyVolume 5, Issue 3, pages 191-196, 1995) V30M CCTGCCATCAATGTGGCC ATGCATGTGTTCAGAAAGGCT allele CCTGCCATCAATGTGGCC G TGCATGTGTTCAGAAAGGCT WTallele 

Example 20 Therapeutic Application of the CRISPR-Cas System in Glaucoma,Amyloidosis, and Huntington's Disease

Glaucoma: Applicants design guide RNAs to target the first exon of themycilin (MYOC) gene. Applicants use adenovirus vectors (Ad5) to packageboth Cas9 as well as a guide RNA targeting the MYOC gene. Applicantsinject adenoviral vectors into the trabecular meshwork where cells havebeen implicated in the pathophysiology of glaucoma. Applicants initiallytest this out in mouse models carrying the mutated MYOC gene to seewhether they improve visual acuity and decrease pressure in the eyes.Therapeutic application in humans employ a similar strategy.

Amyloidosis: Applicants design guide RNAs to target the first exon ofthe transthyretin (TTR) gene in the liver. Applicants use AAV8 topackage Cas9 as well as guide RNA targeting the first exon of the TTRgene. AAV8 has been shown to have efficient targeting of the liver andwill be administered intravenously. Cas9 can be driven either usingliver specific promoters such as the albumin promoter, or using aconstitutive promoter. A pol3 promoter drives the guide RNA.

Alternatively, Applicants utilize hydrodynamic delivery of plasmid DNAto knockout the TTR gene. Applicants deliver a plasmid encoding Cas9 andthe guideRNA targeting Exon1 of TTR.

As a further alternative approach, Applicants administer a combinationof RNA (mRNA for Cas9, and guide RNA). RNA can be packaged usingliposomes such as Invivofectamine from Life Technologies and deliveredintravenously. To reduce RNA-induced immunogenicity, increase the levelof Cas9 expression and guide RNA stability, Applicants modify the Cas9mRNA using 5′ capping. Applicants also incorporate modified RNAnucleotides into Cas9 mRNA and guide RNA to increase their stability andreduce immunogenicity (e.g. activation of TLR). To increase efficiency,Applicants administer multiple doses of the virus, DNA, or RNA.

Huntington's Disease: Applicants design guide RNA based on allelespecific mutations in the HTT gene of patients. For example, in apatient who is heterozygous for HTT with expanded CAG repeat, Applicantsidentify nucleotide sequences unique to the mutant HTT allele and use itto design guideRNA. Applicants ensure that the mutant base is locatedwithin the last 9 bp of the guide RNA (which Applicants have ascertainedhas the ability to discriminate between single DNA base mismatchesbetween the target size and the guide RNA).

Applicants package the mutant HTT allele specific guide RNA and Cas9into AAV9 and deliver into the striatum of Huntington's patients. Virusis injected into the striatum stereotactically via a craniotomy. AAV9 isknown to transduce neurons efficiently. Applicants drive Cas9 using aneuron specific promoter such as human Synapsin 1.

Example 21 Therapeutic Application of the CRISPR-Cas System in HIV

Chronic viral infection is a source of significant morbidity andmortality. While there exists for many of these viruses conventionalantiviral therapies that effectively target various aspects of viralreplication, current therapeutic modalities are usually non-curative innature due to “viral latency.” By its nature, viral latency ischaracterized by a dormant phase in the viral life cycle without activeviral production. During this period, the virus is largely able to evadeboth immune surveillance and conventional therapeutics allowing for itto establish long-standing viral reservoirs within the host from whichsubsequent re-activation can permit continued propagation andtransmission of virus. Key to viral latency is the ability to stablymaintain the viral genome, accomplished either through episomal orproviral latency, which stores the viral genome in the cytoplasm orintegrates it into the host genome, respectively. In the absence ofeffective vaccinations which would prevent primary infection, chronicviral infections characterized by latent reservoirs and episodes oflytic activity can have significant consequences: human papilloma virus(HPV) can result in cervical cancer, hepatitis C virus (HCV) predisposesto hepatocellular carcinoma, and human immunodeficiency virus eventuallydestroys the host immune system resulting in susceptibility toopportunistic infections. As such, these infections require life-longuse of currently available antiviral therapeutics. Further complicatingmatters is the high mutability of many of these viral genomes which leadto the evolution of resistant strains for which there exists noeffective therapy.

The CRISPR-Cas system is a bacterial adaptive immune system able toinduce double-stranded DNA breaks (DSB) in a multiplex-able,sequence-specific manner and has been recently re-constituted withinmammalian cell systems. It has been shown that targeting DNA with one ornumerous guide-RNAs can result in both indels and deletions of theintervening sequences, respectively. As such, this new technologyrepresents a means by which targeted and multiplexed DNA mutagenesis canbe accomplished within a single cell with high efficiency andspecificity. Consequently, delivery of the CRISPR-Cas system directedagainst viral DNA sequences could allow for targeted disruption anddeletion of latent viral genomes even in the absence of ongoing viralproduction.

As an example, chronic infection by HIV-1 represents a global healthissue with 33 million individuals infected and an annual incidence of2.6 million infections. The use of the multimodal highly activeantiretroviral therapy (HAART), which simultaneously targets multipleaspects of viral replication, has allowed HIV infection to be largelymanaged as a chronic, not terminal, illness. Without treatment,progression of HIV to AIDS occurs usually within 9-10 years resulting indepletion of the host immune system and occurrence of opportunisticinfections usually leading to death soon thereafter. Secondary to virallatency, discontinuation of HAART invariably leads to viral rebound.Moreover, even temporary disruptions in therapy can select for resistantstrains of HIV uncontrollable by available means. Additionally, thecosts of HAART therapy are significant: within the US $10,000-15,0000per person per year. As such, treatment approaches directly targetingthe HIV genome rather than the process of viral replication represents ameans by which eradication of latent reservoirs could allow for acurative therapeutic option.

Development and delivery of an HIV-1 targeted CRISPR-Cas systemrepresents a unique approach differentiable from existing means oftargeted DNA mutagenesis, i.e. ZFN and TALENs, with numerous therapeuticimplications. Targeted disruption and deletion of the HIV-1 genome byCRISPR-mediated DSB and indels in conjunction with HAART could allow forsimultaneous prevention of active viral production as well as depletionof latent viral reservoirs within the host.

Once integrated within the host immune system, the CRISPR-Cas systemallows for generation of a HIV-1 resistant sub-population that, even inthe absence of complete viral eradication, could allow for maintenanceand re-constitution of host immune activity. This could potentiallyprevent primary infection by disruption of the viral genome preventingviral production and integration, representing a means to “vaccination”.Multiplexed nature of the CRISPR-Cas system allows targeting of multipleaspects of the genome simultaneously within individual cells.

As in HAART, viral escape by mutagenesis is minimized by requiringacquisition of multiple adaptive mutations concurrently. Multiplestrains of HIV-1 can be targeted simultaneously which minimizes thechance of super-infection and prevents subsequent creation of newrecombinants strains. Nucleotide, rather than protein, mediatedsequence-specificity of the CRISPR-Cas system allows for rapidgeneration of therapeutics without need for significantly alteringdelivery mechanism.

In order to accomplish this, Applicants generate CRISPR-Cas guide RNAsthat target the vast majority of the HIV-1 genome while taking intoaccount HIV-1 strain variants for maximal coverage and effectiveness.Sequence analyses of genomic conservation between HIV-1 subtypes andvariants should allow for targeting of flanking conserved regions of thegenome with the aims of deleting intervening viral sequences orinduction of frame-shift mutations which would disrupt viral genefunctions.

Applicants accomplish delivery of the CRISPR-Cas system by conventionaladenoviral or lentiviral-mediated infection of the host immune system.Depending on approach, host immune cells could be a) isolated,transduced with CRISPR-Cas, selected, and re-introduced in to the hostor b) transduced in vivo by systemic delivery of the CRISPR-Cas system.The first approach allows for generation of a resistant immunepopulation whereas the second is more likely to target latent viralreservoirs within the host.

Examples of potential HIV-1 targeted spacers adapted fromMcintyre et al, which generated shRNAs against HIV-1optimized for maximal coverage of HIV-1 variants.CACTGCTTAAGCCTCGCTCGAGG TCACCAGCAATATTCGCTCGAGG CACCAGCAATATTCCGCTCGAGGTAGCAACAGACATACGCTCGAGG GGGCAGTAGTAATACGCTCGAGG CCAATTCCCATACATTATTGTAC

Example 22 Targeted Correction of deltaF508 or Other Mutations in CysticFibrosis

An aspect of the invention provides for a pharmaceutical compositionthat may comprise an CRISPR-Cas gene therapy particle and abiocompatible pharmaceutical carrier. According to another aspect, amethod of gene therapy for the treatment of a subject having a mutationin the CFTR gene comprises administering a therapeutically effectiveamount of a CRISPR-Cas gene therapy particle to the cells of a subject.

This Example demonstrates gene transfer or gene delivery of a CRISPR-Cassystem in airways of subject or a patient in need thereof, sufferingfrom cystic fibrosis or from cystic fibrosis related symptoms, usingadeno-associated virus (AAV) particles.

Study Design: Subjects or patients in need there of: Human, non-primatehuman, canine, feline, bovine, equine and other domestic animals,related. This study tests efficacy of gene transfer of a CRISPR-Cassystem by a AAV vector. Applicants determine transgene levels sufficientfor gene expression and utilize a CRISPR-Cas system comprising a Cas9enzyme to target deltaF508 or other CFTR-inducing mutations.

The treated subjects receive pharmaceutically effective amount ofaerosolized AAV vector system per lung endobronchially delivered whilespontaneously breathing. The control subjects receive equivalent amountof a pseudotyped AAV vector system with an internal control gene. Thevector system may be delivered along with a pharmaceutically acceptableor biocompatible pharmaceutical carrier. Three weeks or an appropriatetime interval following vector administration, treated subjects aretested for amelioration of cystic fibrosis related symptoms.

Applicants use an adenovirus or an AAV particle.

Applicants clone the following gene constructs, each operably linked toone or more regulatory sequences (Cbh or EF1a promoter for Cas9, U6 orH1 promoter for chimeric guide RNA), into one or more adenovirus or AAVvectors or any other compatible vector: A CFTRdelta508 targetingchimeric guide RNA (FIG. 31B), a repair template for deltaF508 mutation(FIG. 31C) and a codon optimized Cas9 enzyme with optionally one or morenuclear localization signal or sequence(s) (NLS(s)), e.g., two (2) NLSs.

Identification of Cas9 Target Site

Applicants analyzed the human CFTR genomic locus and identified the Cas9target site (FIG. 31A). (PAM may contain a NGG or a NNAGAAW motif).

Gene Repair Strategy

Applicants introduce an adenovirus/AAV vector system comprising a Cas9(or Cas9 nickase) and the guide RNA along with a adenovirus/AAV vectorsystem comprising the homology repair template containing the F508residue into the subject via one of the methods of delivery discussedearlier. The CRISPR-Cas system is guided by the CFTRdelta 508 chimericguide RNA and targets a specific site of the CFTR genomic locus to benicked or cleaved. After cleavage, the repair template is inserted intothe cleavage site via homologous recombination correcting the deletionthat results in cystic fibrosis or causes cystic fibrosis relatedsymptoms. This strategy to direct delivery and provide systemicintroduction of CRISPR systems with appropriate guide RNAs can beemployed to target genetic mutations to edit or otherwise manipulategenes that cause metabolic, liver, kidney and protein diseases anddisorders such as those in Table B.

Example 23 Generation of Gene Knockout Cell Library

This example demonstrates how to generate a library of cells where eachcell has a single gene knocked out:

Applicants make a library of ES cells where each cell has a single geneknocked out, and the entire library of ES cells will have every singlegene knocked out. This library is useful for the screening of genefunction in cellular processes as well as diseases.

To make this cell library, Applicants integrate Cas9 driven by aninducible promoter (e.g. doxycycline inducible promoter) into the EScell. In addition, Applicants integrate a single guide RNA targeting aspecific gene in the ES cell. To make the ES cell library, Applicantssimply mix ES cells with a library of genes encoding guide RNAstargeting each gene in the human genome. Applicants first introduce asingle BxB1 attB site into the AAVS1 locus of the human ES cell. ThenApplicants use the BxB1 integrase to facilitate the integration ofindividual guide RNA genes into the BxB1 attB site in AAVS1 locus. Tofacilitate integration, each guide RNA gene is contained on a plasmidthat carries of a single attP site. This way BxB1 will recombine theattB site in the genome with the attP site on the guide RNA containingplasmid.

To generate the cell library, Applicants take the library of cells thathave single guide RNAs integrated and induce Cas9 expression. Afterinduction, Cas9 mediates double strand break at sites specified by theguide RNA. To verify the diversity of this cell library, Applicantscarry out whole exome sequencing to ensure that Applicants are able toobserve mutations in every single targeted gene. This cell library canbe used for a variety of applications, including whole library-basedscreens, or can be sorted into individual cell clones to facilitaterapid generation of clonal cell lines with individual human genesknocked out.

Example 24 Engineering of Microalgae Using Cas9

Methods of Delivering Cas9

Method 1: Applicants deliver Cas9 and guide RNA using a vector thatexpresses Cas9 under the control of a constitutive promoter such asHsp70A-Rbc S2 or Beta2-tubulin.

Method 2: Applicants deliver Cas9 and T7 polymerase using vectors thatexpresses Cas9 and T7 polymerase under the control of a constitutivepromoter such as Hsp70A-Rbc S2 or Beta2-tubulin. Guide RNA will bedelivered using a vector containing T7 promoter driving the guide RNA.

Method 3: Applicants deliver Cas9 mRNA and in vitro transcribed guideRNA to algae cells. RNA can be in vitro transcribed. Cas9 mRNA willconsist of the coding region for Cas9 as well as 3′UTR from Cop1 toensure stabilization of the Cas9 mRNA.

For Homologous recombination, Applicants provide an additional homologydirected repair template.

Sequence for a cassette driving the expression of Cas9 under the controlof beta-2 tubulin promoter, followed by the 3′ UTR of Cop1.

TCTTTCTTGCGCTATGACACTTCCAGCAAAAGGTAGGGCGGGCTGCGAGACGGCTTCCCGGCGCTGCATGCAACACCGATGATGCTTCGACCCCCCGAAGCTCCTTCGGGGCTGCATGGGCGCTCCGATGCCGCTCCAGGGCGAGCGCTGTTTAAATAGCCAGGCCCCCGATTGCAAAGACATTATAGCGAGCTACCAAAGCCATATTCAAACACCTAGATCACTACCACTTCTACACAGGCCACTCGAGCTTGTGATCGCACTCCGCTAAGGGGGCGCCTCTTCCTCTTCGTTTCAGTCACAACCCGCAAACATGTACCCATACGATGTTCCAGATTACGCTTCGCCGAAGAAAAAGCGCAAGGTCGAAGCGTCCGACAAGAAGTACAGCATCGGCCTGGACATCGGCACCAACTCTGTGGGCTGGGCCGTGATCACCGACGAGTACAAGGTGCCCAGCAAGAAATTCAAGGTGCTGGGCAACACCGACCGGCACAGCATCAAGAAGAACCTGATCGGAGCCCTGCTGTTCGACAGCGGCGAAACAGCCGAGGCCACCCGGCTGAAGAGAACCGCCAGAAGAAGATACACCAGACGGAAGAACCGGATCTGCTATCTGCAAGAGATCTTCAGCAACGAGATGGCCAAGGTGGACGACAGCTTCTTCCACAGACTGGAAGAGTCCTTCCTGGTGGAAGAGGATAAGAAGCACGAGCGGCACCCCATCTTCGGCAACATCGTGGACGAGGTGGCCTACCACGAGAAGTACCCCACCATCTACCACCTGAGAAAGAAACTGGTGGACAGCACCGACAAGGCCGACCTGCGGCTGATCTATCTGGCCCTGGCCCACATGATCAAGTTCCGGGGCCACTTCCTGATCGAGGGCGACCTGAACCCCGACAACAGCGACGTGGACAAGCTGTTCATCCAGCTGGTGCAGACCTACAACCAGCTGTTCGAGGAAAACCCCATCAACGCCAGCGGCGTGGACGCCAAGGCCATCCTGTCTGCCAGACTGAGCAAGAGCAGACGGCTGGAAAATCTGATCGCCCAGCTGCCCGGCGAGAAGAAGAATGGCCTGTTCGGCAACCTGATTGCCCTGAGCCTGGGCCTGACCCCCAACTTCAAGAGCAACTTCGACCTGGCCGAGGATGCCAAACTGCAGCTGAGCAAGGACACCTACGACGACGACCTGGACAACCTGCTGGCCCAGATCGGCGACCAGTACGCCGACCTGTTTCTGGCCGCCAAGAACCTGTCCGACGCCATCCTGCTGAGCGACATCCTGAGAGTGAACACCGAGATCACCAAGGCCCCCCTGAGCGCCTCTATGATCAAGAGATACGACGAGCACCACCAGGACCTGACCCTGCTGAAAGCTCTCGTGCGGCAGCAGCTGCCTGAGAAGTACAAAGAGATTTTCTTCGACCAGAGCAAGAACGGCTACGCCGGCTACATTGACGGCGGAGCCAGCCAGGAAGAGTTCTACAAGTTCATCAAGCCCATCCTGGAAAAGATGGACGGCACCGAGGAACTGCTCGTGAAGCTGAACAGAGAGGACCTGCTGCGGAAGCAGCGGACCTTCGACAACGGCAGCATCCCCCACCAGATCCACCTGGGAGAGCTGCACGCCATTCTGCGGCGGCAGGAAGATTTTTACCCATTCCTGAAGGACAACCGGGAAAAGATCGAGAAGATCCTGACCTTCCGCATCCCCTACTACGTGGGCCCTCTGGCCAGGGGAAACAGCAGATTCGCCTGGATGACCAGAAAGAGCGAGGAAACCATCACCCCCTGGAACTTCGAGGAAGTGGTGGACAAGGGCGCTTCCGCCCAGAGCTTCATCGAGCGGATGACCAACTTCGATAAGAACCTGCCCAACGAGAAGGTGCTGCCCAAGCACAGCCTGCTGTACGAGTACTTCACCGTGTATAACGAGCTGACCAAAGTGAAATACGTGACCGAGGGAATGAGAAAGCCCGCCTTCCTGAGCGGCGAGCAGAAAAAGGCCATCGTGGACCTGCTGTTCAAGACCAACCGGAAAGTGACCGTGAAGCAGCTGAAAGAGGACTACTTCAAGAAAATCGAGTGCTTCGACTCCGTGGAAATCTCCGGCGTGGAAGATCGGTTCAACGCCTCCCTGGGCACATACCACGATCTGCTGAAAATTATCAAGGACAAGGACTTCCTGGACAATGAGGAAAACGAGGACATTCTGGAAGATATCGTGCTGACCCTGACACTGTTTGAGGACAGAGAGATGATCGAGGAACGGCTGAAAACCTATGCCCACCTGTTCGACGACAAAGTGATGAAGCAGCTGAAGCGGCGGAGATACACCGGCTGGGGCAGGCTGAGCCGGAAGCTGATCAACGGCATCCGGGACAAGCAGTCCGGCAAGACAATCCTGGATTTCCTGAAGTCCGACGGCTTCGCCAACAGAAACTTCATGCAGCTGATCCACGACGACAGCCTGACCTTTAAAGAGGACATCCAGAAAGCCCAGGTGTCCGGCCAGGGCGATAGCCTGCACGAGCACATTGCCAATCTGGCCGGCAGCCCCGCCATTAAGAAGGGCATCCTGCAGACAGTGAAGGTGGTGGACGAGCTCGTGAAAGTGATGGGCCGGCACAAGCCCGAGAACATCGTGATCGAAATGGCCAGAGAGAACCAGACCACCCAGAAGGGACAGAAGAACAGCCGCGAGAGAATGAAGCGGATCGAAGAGGGCATCAAAGAGCTGGGCAGCCAGATCCTGAAAGAACACCCCGTGGAAAACACCCAGCTGCAGAACGAGAAGCTGTACCTGTACTACCTGCAGAATGGGCGGGATATGTACGTGGACCAGGAACTGGACATCAACCGGCTGTCCGACTACGATGTGGACCATATCGTGCCTCAGAGCTTTCTGAAGGACGACTCCATCGACAACAAGGTGCTGACCAGAAGCGACAAGAACCGGGGCAAGAGCGACAACGTGCCCTCCGAAGAGGTCGTGAAGAAGATGAAGAACTACTGGCGGCAGCTGCTGAACGCCAAGCTGATTACCCAGAGAAAGTTCGACAATCTGACCAAGGCCGAGAGAGGCGGCCTGAGCGAACTGGATAAGGCCGGCTTCATCAAGAGACAGCTGGTGGAAACCCGGCAGATCACAAAGCACGTGGCACAGATCCTGGACTCCCGGATGAACACTAAGTACGACGAGAATGACAAGCTGATCCGGGAAGTGAAAGTGATCACCCTGAAGTCCAAGCTGGTGTCCGATTTCCGGAAGGATTTCCAGTTTTACAAAGTGCGCGAGATCAACAACTACCACCACGCCCACGACGCCTACCTGAACGCCGTCGTGGGAACCGCCCTGATCAAAAAGTACCCTAAGCTGGAAAGCGAGTTCGTGTACGGCGACTACAAGGTGTACGACGTGCGGAAGATGATCGCCAAGAGCGAGCAGGAAATCGGCAAGGCTACCGCCAAGTACTTCTTCTACAGCAACATCATGAACTTTTTCAAGACCGAGATTACCCTGGCCAACGGCGAGATCCGGAAGCGGCCTCTGATCGAGACAAACGGCGAAACCGGGGAGATCGTGTGGGATAAGGGCCGGGATTTTGCCACCGTGCGGAAAGTGCTGAGCATGCCCCAAGTGAATATCGTGAAAAAGACCGAGGTGCAGACAGGCGGCTTCAGCAAAGAGTCTATCCTGCCCAAGAGGAACAGCGATAAGCTGATCGCCAGAAAGAAGGACTGGGACCCTAAGAAGTACGGCGGCTTCGACAGCCCCACCGTGGCCTATTCTGTGCTGGTGGTGGCCAAAGTGGAAAAGGGCAAGTCCAAGAAACTGAAGAGTGTGAAAGAGCTGCTGGGGATCACCATCATGGAAAGAAGCAGCTTCGAGAAGAATCCCATGCTGCCTAAGTACTCCCTGTTCGAGCTGGAAAACGGCCGGAAGAGAATGCTGGCCTCTGCCGGCGAACTGCAGAAGGGAAACGAACTGGCCCTGCCCTCCAAATATGTGAACTTCCTGTACCTGGCCAGCCACTATGAGAAGCTGAAGGGCTCCCCCGAGGATAATGAGCAGAAACAGCTGTTTGTGGAACAGCACAAGCACTACCTGGACGAGATCATCGAGCAGATCAGCGAGTTCTCCAAGAGAGTGATCCTGGCCGACGCTAATCTGGACAAAGTGCTGTCCGCCTACAACAAGCACCGGGATAAGCCCATCAGAGAGCAGGCCGAGAATATCATCCACCTGTTTACCCTGACCAATCTGGGAGCCCCTGCCGCCTTCAAGTACTTTGACACCACCATCGACCGGAAGAGGTACACCAGCACCAAAGAGGTGCTGGACGCCACCCTGATCCACCAGAGCATCACCGGCCTGTACGAGACACGGATCGACCTGTCTCAGCTGGGAGGCGACAGCCCCAAGAAGAAGAGAAAGGTGGAGGCCAGCTAAGGATCCGGCAAGACTGGCCCCGCTTGGCAACGCAACAGTGAGCCCCTCCCTAGTGTGTTTGGGGATGTGACTATGTATTCGTGTGTTGGCCAACGGGTCAACCCGAACAGATTGATACCCGCCTTGGCATTTCCTGTCAGAATGTAACGTCAGTTGATGGTACT

Sequence for a cassette driving the expression of T7 polymerase underthe control of beta-2 tubulin promoter, followed by the 3′ UTR of Cop1:

TCTTTCTTGCGCTATGACACTTCCAGCAAAAGGTAGGGCGGGCTGCGAGACGGCTTCCCGGCGCTGCATGCAACACCGATGATGCTTCGACCCCCCGAAGCTCCTTCGGGGCTGCATGGGCGCTCCGATGCCGCTCCAGGGCGAGCGCTGTTTAAATAGCCAGGCCCCCGATTGCAAAGACATTATAGCGAGCTACCAAAGCCATATTCAAACACCTAGATCACTACCACTTCTACACAGGCCACTCGAGCTTGTGATCGCACTCCGCTAAGGGGGCGCCTCTTCCTCTTCGTTTCAGTCACAACCCGCAAACatgcctaagaagaagaggaaggttaacacgattaacatcgctaagaacgacttctctgacatcgaactggctgctatcccgttcaacactctggctgaccattacggtgagcgtttagctcgcgaacagttggcccttgagcatgagtcttacgagatgggtgaagcacgcttccgcaagatgtagagcgtcaacttaaagctggtgaggttgcggataacgctgccgccaagcctctcatcactaccctactccctaagatgattgcacgcatcaacgactggtttgaggaagtgaaagctaagcgcggcaagcgcccgacagccttccagttcctgcaagaaatcaagccggaagccgtagcgtacatcaccattaagaccactctggcttgcctaaccagtgctgacaatacaaccgttcaggctgtagcaagcgcaatcggtcgggccattgaggacgaggctcgcttcggtcgtatccgtgaccttgaagctaagcacttcaagaaaaacgttgaggaacaactcaacaagcgcgtagggcacgtctacaagaaagcatttatgcaagttgtcgaggctgacatgctctctaagggtctactcggtggcgaggcgtggtcttcgtggcataaggaagactctattcatgtaggagtacgcgcatcgagatgctcattgagtcaaccggaatggttagcttacaccgccaaaatgctggcgtagtaggtcaagactctgagactatcgaactcgcacctgaatacgctgaggctatcgcaacccgtgcaggtgcgctggctggcatctctccgatgttccaaccttgcgtagttcctcctaagccgtggactggcattactggtggtggctattgggctaacggtcgtcgtcctctggcgctggtgcgtactcacagtaagaaagcactgatgcgctacgaagacgtttacatgcctgaggtgtacaaagcgattaacattgcgcaaaacaccgcatggaaaatcaacaagaaagtcctagcggtcgccaacgtaatcaccaagtggaagcattgtccggtcgaggacatccctgcgattgagcgtgaagaactcccgatgaaaccggaagacatcgacatgaatcctgaggctctcaccgcgtggaaacgtgctgccgctgctgtgtaccgcaaggacaaggctcgcaagtctcgccgtatcagccttgagttcatgcttgagcaagccaataagtttgctaaccataaggccatctggttcccttacaacatggactggcgcggtcgtgtttacgctgtgtcaatgttcaacccgcaaggtaacgatatgaccaaaggactgcttacgctggcgaaaggtaaaccaatcggtaaggaaggttactactggctgaaaatccacggtgcaaactgtgcgggtgtcgacaaggttccgttccctgagcgcatcaagttcattgaggaaaaccacgagaacatcatggcttgcgctaagtctccactggagaacacttggtgggctgagcaagattctccgttctgcttccttgcgttctgctttgagtacgctggggtacagcaccacggcctgagctataactgctcccttccgctggcgtttgacgggtcttgctctggcatccagcacttctccgcgatgctccgagatgaggtaggtggtcgcgcggttaacttgcttcctagtgaaaccgttcaggacatctacgggattgttgctaagaaagtcaacgagattctacaagcagacgcaatcaatgggaccgataacgaagtagttaccgtgaccgatgagaacactggtgaaatctctgagaaagtcaagctgggcactaaggcactggctggtcaatggctggcttacggtgttactcgcagtgtgactaagcgttcagtcatgacgctggcttacgggtccaaagagttcggcttccgtcaacaagtgctggaagataccattcagccagctattgattccggcaagggtctgatgttcactcagccgaatcaggctgctggatacatggctaagctgatttgggaatctgtgagcgtgacggtggtagctgcggttgaagcaatgaactggcttaagtctgctgctaagctgctggctgctgaggtcaaagataagaagactggagagattcttcgcaagcgttgcgctgtgcattgggtaactcctgatggtttccctgtgtggcaggaatacaagaagcctattcagacgcgcttgaacctgatgttcctcggtcagttccgcttacagcctaccattaacaccaacaaagatagcgagattgatgcacacaaacaggagtctggtatcgctcctaactttgtacacagccaagacggtagccaccttcgtaagactgtagtgtgggcacacgagaagtacggaatcgaatcttttgcactgattcacgactccttcggtacgattccggctgacgctgcgaacctgttcaaagcagtgcgcgaaactatggttgacacatatgagtcttgtgatgtactggctgatttctacgaccagttcgctgaccagttgcacgagtctcaattggacaaaatgccagcacttccggctaaaggtaacttgaacctccgtgacatcttagagtcggacttcgcgttcgcgtaaGGATCCGGCAAGACTGGCCCCGCTTGGCAACGCAACAGTGAGCCCCTCCCTAGTGTGTTTGGGGATGTGACTATGTATTCGTGTGTTGGCCAACGGGTCAACCCGAACAGATTGATACCCGCCTTGGCATTTCCTGTCAGAATGTAACGTCAGTTGATGGTACT

Sequence of guide RNA driven by the T7 promoter (T7 promoter, Nsrepresent targeting sequence):

gaaatTAATACGACTCACTATA NNNNNNNNNNNNNNNNNNNNgttttagagctaGAAAtagcaagttaaaataaggctagtccgttatcaacttgaaaaagtggcaccgagtcggtgcttttttt

Gene Delivery:

Chlamydomonas reinhardtii strain CC-124 and CC-125 from theChlamydomonas Resource Center will be used for electroporation.Electroporation protocol follows standard recommended protocol from theGeneArt Chlamydomonas Engineering kit.

Also, Applicants generate a line of Chlamydomonas reinhardtii thatexpresses Cas9 constitutively. This can be done by using pChlamy1(linearized using PvuI) and selecting for hygromycin resistant colonies.Sequence for pChlamy1 containing Cas9 is below. In this way to achievegene knockout one simply needs to deliver RNA for the guideRNA. Forhomologous recombination Applicants deliver guideRNA as well as alinearized homologous recombination template.

pChlamy1-Cas9:

TGCGGTATTTCACACCGCATCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTTCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGTTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGTCGCTGAGGCTTGACATGATTGGTGCGTATGTTTGTATGAAGCTACAGGACTGATTTGGCGGGCTATGAGGGCGGGGGAAGCTCTGGAAGGGCCGCGATGGGGCGCGCGGCGTCCAGAAGGCGCCATACGGCCCGCTGGCGGCACCCATCCGGTATAAAAGCCCGCGACCCCGAACGGTGACCTCCACTTTCAGCGACAAACGAGCACTTATACATACGCGACTATTCTGCCGCTATACATAACCACTCAGCTAGCTTAAGATCCCATCAAGCTTGCATGCCGGGCGCGCCAGAAGGAGCGCAGCCAAACCAGGATGATGTTTGATGGGGTATTTGAGCACTTGCAACCCTTATCCGGAAGCCCCCTGGCCCACAAAGGCTAGGCGCCAATGCAAGCAGTTCGCATGCAGCCCCTGGAGCGGTGCCCTCCTGATAAACCGGCCAGGGGGCCTATGTTCTTTACTTTTTTACAAGAGAAGTCACTCAACATCTTAAAATGGCCAGGTGAGTCGACGAGCAAGCCCGGCGGATCAGGCAGCGTGCTTGCAGATTTGACTTGCAACGCCCGCATTGTGTCGACGAAGGCTTTTGGCTCCTCTGTCGCTGTCTCAAGCAGCATCTAACCCTGCGTCGCCGTTTCCATTTGCAGGAGATTCGAGGTACCATGTACCCATACGATGTTCCAGATTACGCTTCGCCGAAGAAAAAGCGCAAGGTCGAAGCGTCCGACAAGAAGTACAGCATCGGCCTGGACATCGGCACCAACTCTGTGGGCTGGGCCGTGATCACCGACGAGTACAAGGTGCCCAGCAAGAAATTCAAGGTGCTGGGCAACACCGACCGGCACAGCATCAAGAAGAACCTGATCGGAGCCCTGCTGTTCGACAGCGGCGAAACAGCCGAGGCCACCCGGCTGAAGAGAACCGCCAGAAGAAGATACACCAGACGGAAGAACCGGATCTGCTATCTGCAAGAGATCTTCAGCAACGAGATGGCCAAGGTGGACGACAGCTTCTTCCACAGACTGGAAGAGTCCTTCCTGGTGGAAGAGGATAAGAAGCACGAGCGGCACCCCATCTTCGGCAACATCGTGGACGAGGTGGCCTACCACGAGAAGTACCCCACCATCTACCACCTGAGAAAGAAACTGGTGGACAGCACCGACAAGGCCGACCTGCGGCTGATCTATCTGGCCCTGGCCCACATGATCAAGTTCCGGGGCCACTTCCTGATCGAGGGCGACCTGAACCCCGACAACAGCGACGTGGACAAGCTGTTCATCCAGCTGGTGCAGACCTACAACCAGCTGTTCGAGGAAAACCCCATCAACGCCAGCGGCGTGGACGCCAAGGCCATCCTGTCTGCCAGACTGAGCAAGAGCAGACGGCTGGAAAATCGATCGCCCAGCTGCCCGGCGAGAAGAAGAATGGCCTGTTCGGCAACCTGATTGCCCTGAGCCTGGGCCTGACCCCCAACTTCAAGAGCAACTTCGACCTGGCCGAGGATGCCAAACTGCAGCTGAGCAAGGACACCTACGACGACGACCTGGACAACCTGCTGGCCCAGATCGGCGACCAGTACGCCGACCTGTTTCTGGCCGCCAAGAACCTGTCCGACGCCATCCTGCTGAGCGACATCCTGAGAGTGAACACCGAGATCACCAAGGCCCCCCTGAGCGCCTCTATGATCAAGAGATACGACGAGCACCACCAGGACCTGACCCTGCTGAAAGCTCTCGTGCGGCAGCAGCTGCCTGAGAAGTACAAAGAGATTTTCTTCGACCAGAGCAAGAACGGCTACGCCGGCTACATTGACGGCGGAGCCAGCCAGGAAGAGTTCTACAAGTTCATCAAGCCCATCCTGGAAAAGATGGACGGCACCGAGGAACTGCTCGTGAAGCTGAACAGAGAGGACCTGCTGCGGAAGCAGCGGACCTTCGACAACGGCAGCATCCCCCACCAGATCCACCTGGGAGAGCTGCACGCCATTCTGCGGCGGCAGGAAGATTTTTACCCATTCCTGAAGGACAACCGGGAAAAGATCGAGAAGATCCTGACCTTCCGCATCCCCTACTACGTGGGCCCTCTGGCCAGGGGAAACAGCAGATTCGCCTGGATGACCAGAAAGAGCGAGGAAACCATCACCCCCTGGAACTTCGAGGAAGTGGTGGACAAGGGCGCTTCCGCCCAGAGCTTCATCGAGCGGATGACCAACTTCGATAAGAACCTGCCCAACGAGAAGGTGCTGCCCAAGCACAGCCTGCTGTACGAGTACTTCACCGTGTATAACGAGCTGACCAAAGTGAAATACGTGACCGAGGGAATGAGAAAGCCCGCCTTCCTGAGCGGCGAGCAGAAAAAGGCCATCGTGGACCTGCTGTTCAAGACCAACCGGAAAGTGACCGTGAAGCAGCTGAAAGAGGACTACTTCAAGAAAATCGAGTGCTTCGACTCCGTGGAAATCTCCGGCGTGGAAGATCGGTTCAACGCCTCCCTGGGCACATACCACGATCTGCTGAAAATTATCAAGGACAAGGACTTCCTGGACAATGAGGAAAACGAGGACATTCTGGAAGATATCGTGCTGACCCTGACACTGTTTGAGGACAGAGAGATGATCGAGGAACGGCTGAAAACCTATGCCCACCTGTTCGACGACAAAGTGATGAAGCAGCTGAAGCGGCGGAGATACACCGGCTGGGGCAGGCTGAGCCGGAAGCTGATCAACGGCATCCGGGACAAGCAGTCCGGCAAGACAATCCTGGATTTCCTGAAGTCCGACGGCTTCGCCAACAGAAACTTCATGCAGCTGATCCACGACGACAGCCTGACCTTTAAAGAGGACATCCAGAAAGCCCAGGTGTCCGGCCAGGGCGATAGCCTGCACGAGCACATTGCCAATCTGGCCGGCAGCCCCGCCATTAAGAAGGGCATCCTGCAGACAGTGAAGGTGGTGGACGAGCTCGTGAAAGTGATGGGCCGGCACAAGCCCGAGAACATCGTGATCGAAATGGCCAGAGAGAACCAGACCACCCAGAAGGGACAGAAGAACAGCCGCGAGAGAATGAAGCGGATCGAAGAGGGCATCAAAGAGCTGGGCAGCCAGATCCTGAAAGAACACCCCGTGGAAAACACCCAGCTGCAGAACGAGAAGCTGTACCTGTACTACCTGCAGAATGGGCGGGATATGTACGTGGACCAGGAACTGGACATCAACCGGCTGTCCGACTACGATGTGGACCATATCGTGCCTCAGAGCTTTCTGAAGGACGACTCCATCGACAACAAGGTGCTGACCAGAAGCGACAAGAACCGGGGCAAGAGCGACAACGTGCCCTCCGAAGAGGTCGTGAAGAAGATGAAGAACTACTGGCGGCAGCTGCTGAACGCCAAGCTGATTACCCAGAGAAAGTTCGACAATCTGACCAAGGCCGAGAGAGGCGGCCTGAGCGAACTGGATAAGGCCGGCTTCATCAAGAGACAGCTGGTGGAAACCCGGCAGATCACAAAGCACGTGGCACAGATCCTGGACTCCCGGATGAACACTAAGTACGACGAGAATGACAAGCTGATCCGGGAAGTGAAAGTGATCACCCTGAAGTCCAAGCTGGTGTCCGATTTCCGGAAGGATTTCCAGTTTTACAAAGTGCGCGAGATCAACAACTACCACCACGCCCACGACGCCTACCTGAACGCCGTCGTGGGAACCGCCCTGATCAAAAAGTACCCTAAGCTGGAAAGCGAGTTCGTGTACGGCGACTACAAGGTGTACGACGTGCGGAAGATGATCGCCAAGAGCGAGCAGGAAATCGGCAAGGCTACCGCCAAGTACTTCTTCTACAGCAACATCATGAACTTTTTCAAGACCGAGATTACCCTGGCCAACGGCGAGATCCGGAAGCGGCCTCTGATCGAGACAAACGGCGAAACCGGGGAGATCGTGTGGGATAAGGGCCGGGATTTTGCCACCGTGCGGAAAGTGCTGAGCATGCCCCAAGTGAATATCGTGAAAAAGACCGAGGTGCAGACAGGCGGCTTCAGCAAAGAGTCTATCCTGCCCAAGAGGAACAGCGATAAGCTGATCGCCAGAAAGAAGGACTGGGACCCTAAGAAGTACGGCGGCTTCGACAGCCCCACCGTGGCCTATTCTGTGCTGGTGGTGGCCAAAGTGGAAAAGGGCAAGTCCAAGAAACTGAAGAGTGTGAAAGAGCTGCTGGGGATCACCATCATGGAAAGAAGCAGCTTCGAGAAGAATCCCATCGACTTTCTGGAAGCCAAGGGCTACAAAGAAGTGAAAAAGGACCTGATCATCAAGCTGCCTAAGTACTCCCTGTTCGAGCTGGAAAACGGCCGGAAGAGAATGCTGGCCTCTGCCGGCGAACTGCAGAAGGGAAACGAACTGGCCCTGCCCTCCAAATATGTGAACTTCCTGTACCTGGCCAGCCACTATGAGAAGCTGAAGGGCTCCCCCGAGGATAATGAGCAGAAACAGCTGTTTGTGGAACAGCACAAGCACTACCTGGACGAGATCATCGAGCAGATCAGCGAGTTCTCCAAGAGAGTGATCCTGGCCGACGCTAATCTGGACAAAGTGCTGTCCGCCTACAACAAGCACCGGGATAAGCCCATCAGAGAGCAGGCCGAGAATATCATCCACCTGTTTACCCTGACCAATCTGGGAGCCCCTGCCGCCTTCAAGTACTTTGACACCACCATCGACCGGAAGAGGTACACCAGCACCAAAGAGGTGCTGGACGCCACCCTGATCCACCAGAGCATCACCGGCCTGTACGAGACACGGATCGACCTGTCTCAGCTGGGAGGCGACAGCCCCAAGAAGAAGAGAAAGGTGGAGGCCAGCTAACATATGATTCGAATGTCTTTCTTGCGCTATGACACTTCCAGCAAAAGGTAGGGCGGGCTGCGAGACGGCTTCCCGGCGCTGCATGCAACACCGATGATGCTTCGACCCCCCGAAGCTCCTTCGGGGCTGCATGGGCGCTCCGATGCCGCTCCAGGGCGAGCGCTGTTTAAATAGCCAGGCCCCCGATTGCAAAGACATTATAGCGAGCTACCAAAGCCATATTCAAACACCTAGATCACTACCACTTCTACACAGGCCACTCGAGCTTGTGATCGCACTCCGCTAAGGGGGCGCCTCTTCCTCTTCGTTTCAGTCACAACCCGCAAACATGACACAAGAATCCCTGTTACTTCTCGACCGTATTGATTCGGATGATTCCTACGCGAGCCTGCGGAACGACCAGGAATTGTGGGAGGTGAGTCGACGAGCAAGCCCGGCGGATCAGGCAGCGTGCTTGCAGATTTGACTTGCAACGCCCGCATTGTGTCGACGAAGGCTTTTGGCTCCTCTGTCGCTGTCTCAAGCAGCATCTAACCCTGCGTCGCCGTTTCCATTTGCAGCCGCTGGCCCGCCGAGCCCTGGAGGAGCTCGGGCTGCCGGTGCCGCCGGTGCTGCGGGTGCCCGGCGAGAGCACCAACCCCGTACTGGTCGGCGAGCCCGGCCCGGTGATCAAGCTGTTCGGCGAGCACTGGTGCGGTCCGGAGAGCCTCGCGTCGGAGTCGGAGGCGTACGCGGTCCTGGCGGACGCCCCGGTGCCGGTGCCCCGCCTCCTCGGCCGCGGCGAGCTGCGGCCCGGCACCGGAGCCTGGCCGTGGCCCTACCTGGTGATGAGCCGGATGACCGGCACCACCTGGCGGTCCGCGATGGACGGCACGACCGACCGGAACGCGCTGCTCGCCCTGGCCCGCGAACTCGGCCGGGTGCTCGGCCGGCTGCACAGGGTGCCGCTGACCGGGAACACCGTGCTCACCCCCCATTCCGAGGTCTTCCCGGAACTGCTGCGGGAACGCCGCGCGGCGACCGTCGAGGACCACCGCGGGTGGGGCTACCTCTCGCCCCGGCTGCTGGACCGCCTGGAGGACTGGCTGCCGGACGTGGACACGCTGCTGGCCGGCCGCGAACCCCGGTTCGTCCACGGCGACCTGCACGGGACCAACATCTTCGTGGACCTGGCCGCGACCGAGGTCACCGGGATCGTCGACTTCACCGACGTCTATGCGGGAGACTCCCGCTACAGCCTGGTGCAACTGCATCTCAACGCCTTCCGGGGCGACCGCGAGATCCTGGCCGCGCTGCTCGACGGGGCGCAGTGGAAGCGGACCGAGGACTTCGCCCGCGAACTGCTCGCCTTCACCTTCCTGCACGACTTCGAGGTGTTCGAGGAGACCCCGCTGGATCTCTCCGGCTTCACCGATCCGGAGGAACTGGCGCAGTTCCTCTGGGGGCCGCCGGACACCGCCCCCGGCGCCTGATAAGGATCCGGCAAGACTGGCCCCGCTTGGCAACGCAACAGTGAGCCCCTCCCTAGTGTGTTTGGGGATGTGACTATGTATTCGTGTGTTGGCCAACGGGTCAACCCGAACAGATTGATACCCGCCTTGGCATTTCCTGTCAGAATGTAACGTCAGTTGATGG TACT

For all modified Chlamydomonas reinhardtii cells, Applicants use PCR,SURVEYOR nuclease assay, and DNA sequencing to verify successfulmodification.

Example 25 Use of Cas9 to Target a Variety of Disease Types

Diseases that involve mutations in protein coding sequence:

Dominant disorders may be targeted by inactivating the dominant negativeallele. Applicants use Cas9 to target a unique sequence in the dominantnegative allele and introduce a mutation via NHEJ. The NHEJ-inducedindel may be able to introduce a frame-shift mutation in the dominantnegative allele and eliminate the dominant negative protein. This maywork if the gene is haplo-sufficient (e.g. MYOC mutation inducedglaucoma and Huntington's disease).

Recessive disorders may be targeted by repairing the disease mutation inboth alleles. For dividing cells, Applicants use Cas9 to introducedouble strand breaks near the mutation site and increase the rate ofhomologous recombination using an exogenous recombination template. Fordividing cells, this may be achieved using multiplexed nickase activityto catalyze the replacement of the mutant sequence in both alleles viaNHEJ-mediated ligation of an exogenous DNA fragment carryingcomplementary overhangs.

Applicants also use Cas9 to introduce protective mutations (e.g.inactivation of CCR5 to prevent HIV infection, inactivation of PCSK9 forcholesterol reduction, or introduction of the A673T into APP to reducethe likelihood of Alzheimer's disease).

Diseases that Involve Non-Coding Sequences

Applicants use Cas9 to disrupt non-coding sequences in the promoterregion, to alter transcription factor binding sites and alter enhanceror repressor elements. For example, Cas9 may be used to excise out theKlf1 enhancer EHS1 in hematopoietic stem cells to reduce BCL11a levelsand reactivate fetal globin gene expression in differentiatederythrocytes

Applicants also use Cas9 to disrupt functional motifs in the 5′ or 3′untranslated regions. For example, for the treatment of myotonicdystrophy, Cas9 may be used to remove CTG repeat expansions in the DMPKgene.

Example 26 Multiplexed Nickase

Aspects of optimization and the teachings of Cas9 detailed in thisapplication may also be used to generate Cas9 nickases. Applicants useCas9 nickases in combination with pairs of guide RNAs to generate DNAdouble strand breaks with defined overhangs. When two pairs of guideRNAs are used, it is possible to excise an intervening DNA fragment. Ifan exogenous piece of DNA is cleaved by the two pairs of guide RNAs togenerate compatible overhangs with the genomic DNA, then the exogenousDNA fragment may be ligated into the genomic DNA to replace the excisedfragment. For example, this may be used to remove trinucleotide repeatexpansion in the huntintin (HTT) gene to treat Huntington's Disease.

If an exogenous DNA that bears fewer number of CAG repeats is provided,then it may be able to generate a fragment of DNA that bears the sameoverhangs and can be ligated into the HTT genomic locus and replace theexcised fragment.

HTT locus. . . CCGTGCCGGGCGGGAGACCGCCATGG                       GGCCCGGCTGTGGCTGAGGAGC . . .with. . . GGCACGGCCCGCCCTCTGGC                         TGGGCCGGGCCGACACCGACTCCTCG . . .fragment excised by Cas9 nickase and two pairs of guide RNAs +exogenous DNA      CGACCCTGGAAA . . . reduced number of CAG repeats . . . CCCCGCCGCCACCCfragment withGGTACCGCTGGGACCTTT . . .                               . . . GGGGCGGCGGfewer number of CAG repeats also cleaved by Cas9 nic- akse and thetwo pairs of guide RNAs

The ligation of the exogenous DNA fragment into the genome does notrequire homologous recombination machineries and therefore this methodmay be used in post-mitotic cells such as neurons.

Example 27 Delivery of CRISPR System

Cas9 and its chimeric guide RNA, or combination of tracrRNA and crRNA,can be delivered either as DNA or RNA. Delivery of Cas9 and guide RNAboth as RNA (normal or containing base or backbone modifications)molecules can be used to reduce the amount of time that Cas9 proteinpersist in the cell. This may reduce the level of off-target cleavageactivity in the target cell. Since delivery of Cas9 as mRNA takes timeto be translated into protein, it might be advantageous to deliver theguide RNA several hours following the delivery of Cas9 mRNA, to maximizethe level of guide RNA available for interaction with Cas9 protein.

In situations where guide RNA amount is limiting, it may be desirable tointroduce Cas9 as mRNA and guide RNA in the form of a DNA expressioncassette with a promoter driving the expression of the guide RNA. Thisway the amount of guide RNA available will be amplified viatranscription.

A variety of delivery systems can be introduced to introduce Cas9 (DNAor RNA) and guide RNA (DNA or RNA) into the host cell. These include theuse of liposomes, viral vectors, electroporation, nanoparticles,nanowires (Shalek et al., Nano Letters, 2012), exosomes. Moleculartrojan horses liposomes (Pardridge et al., Cold Spring Harb Protoc;2010; doi: 10.1101/pdb.prot5407) may be used to deliver Cas9 and guideRNA across the blood brain barrier.

Example 28 Therapeutic Strategies for Trinucleotide Repeat Disorders

As previously mentioned in the application, the target polynucleotide ofa CRISPR complex may include a number of disease-associated genes andpolynucleotides and some of these disease associated gene may belong toa set of genetic disorders referred to as Trinucleotide repeat disorders(referred to as also trinucleotide repeat expansion disorders, tripletrepeat expansion disorders or codon reiteration disorders).

These diseases are caused by mutations in which the trinucleotiderepeats of certain genes exceed the normal, stable threshold which mayusually differ in a gene. The discovery of more repeat expansiondisorders has allowed for the classification of these disorders into anumber of categories based on underlying similar characteristics.Huntington's disease (HD) and the spinocerebellar ataxias that arecaused by a CAG repeat expansion in protein-coding portions of specificgenes are included in Category I. Diseases or disorders with expansionsthat tend to make them phenotypically diverse and include expansions areusually small in magnitude and also found in exons of genes are includedin Category II. Category III includes disorders or diseases which arecharacterized by much larger repeat expansions than either Category I orII and are generally located outside protein coding regions. Examples ofCategory III diseases or disorders include but are not limited toFragile X syndrome, myotonic dystrophy, two of the spinocerebellarataxias, juvenile myoclonic epilepsy, and Friedreich's ataxia.

Similar therapeutic strategies, like the one mentioned for Friedreich'sataxia below may be adopted to address other trinucleotide repeat orexpansion disorders as well. For example, another triple repeat diseasethat can be treated using almost identical strategy is dystrophiamyotonica 1 (DM1), where there is an expanded CTG motif in the 3′ UTR.In Friedreich's ataxia, the disease results from expansion of GAAtrinucleotides in the first intron of frataxin (FXN). One therapeuticstrategy using CRISPR is to excise the GAA repeat from the first intron.The expanded GAA repeat is thought to affect the DNA structure and leadsto recruit the formation of heterochrornatin which turn off the frataxingene (FIG. 32A).

Competitive Advantage over other therapeutic strategies are listedbelow:

siRNA knockdown is not applicable in this case, as disease is due toreduced expression of frataxin. Viral gene therapy is currently beingexplored. HSV-1 based vectors were used to deliver the frataxin gene inanimal models and have shown therapeutic effect. However, long termefficacy of virus-based frataxin delivery suffer from several problems:First, it is difficult to regulate the expression of frataxin to matchnatural levels in health individuals, and second, long term overexpression of frataxin leads to cell death.

Nucleases may be used to excise the GAA repeat to restore healthygenotype, but Zinc Finger Nuclease and TALEN strategies require deliveryof two pairs of high efficacy nucleases, which is difficult for bothdelivery as well as nuclease engineering (efficient excision of genomicDNA by ZFN or TALEN is difficult to achieve).

In contrast to above strategies, the CRISPR-Cas system has clearadvantages. The Cas9 enzyme is more efficient and more multiplexible, bywhich it is meant that one or more targets can be set at the same time.So far, efficient excision of genomic DNA >30% by Cas9 in human cellsand may be as high as 30%, and may be improved in the future.Furthermore, with regard to certain trinucleotide repeat disorders likeHuntington's disease (HD), trinucleotide repeats in the coding regionmay be addressed if there are differences between the two alleles.Specifically, if a HD patient is heterozygous for mutant HTT and thereare nucleotide differences such as SNPs between the wt and mutant HTTalleles, then Cas9 may be used to specifically target the mutant HTTallele. ZFN or TALENs will not have the ability to distinguish twoalleles based on single base differences.

In adopting a strategy using the CRISPR-Cas 9 enzyme to addressFriedreich's ataxia, Applicants design a number of guide RNAs targetingsites flanking the GAA expansion and the most efficient and specificones are chosen (FIG. 32B).

Applicants deliver a combination of guide RNAs targeting the intron I ofFXN along with Cas9 to mediate excision of the GAA expansion region.AAV9 may be used to mediate efficient delivery of Cas9 and in the spinalcord.

If the Alu element adjacent to the GAA expansion is consideredimportant, there may be constraints to the number of sites that can betargeted but Applicants may adopt strategies to avoid disrupting it.

Alternative Strategies:

Rather than modifying the genome using Cas9, Applicants may alsodirectly activate the FXN gene using Cas9 (nuclease activitydeficient)-based DNA binding domain to target a transcription activationdomain to the FXN gene. Applicants may have to address the robustness ofthe Cas9-mediated artificial transcription activation to ensure that itis robust enough as compared to other methods (Tremblay et al.,Transcription Activator-Like Effector Proteins Induce the Expression ofthe Frataxin Gene; Human Gene Therapy. August 2012, 23(8): 883-890.)

Example 29 Strategies for Minimizing Off Target Cleavage Using Cas9Nickase

As previously mentioned in the application, Cas9 may be mutated tomediate single strand cleavage via one or more of the followingmutations: D10A, E762A, and H840A.

To mediate gene knockout via NHEJ, Applicants use a nickase version ofCas9 along with two guide RNAs. Off-target nicking by each individualguide RNA may be primarily repaired without mutation, double strandbreaks (which can lead to mutations via NHEJ) only occur when the targetsites are adjacent to each other. Since double strand breaks introducedby double nicking are not blunt, co-expression of end-processing enzymessuch as TREX1 will increase the level of NHEJ activity.

The following list of targets in tabular form are for genes involved inthe following diseases:

Lafora's Disease—target GSY1 or PPP1R3C (PTG) to reduce glycogen inneurons.

Hypercholesterolemia—target PCSK9

Target sequences are listed in pairs (L and R) with different number ofnucleotides in the spacer (0 to 3 bp). Each spacer may also be used byitself with the wild type Cas9 to introduce double strand break at thetarget locus.

GYS1 (human) GGCC-L ACCCTTGTTAGCCACCTCCC GGCC-R GAACGCAGTGCTCTTCGAAGGGNCC-L CTCACGCCCTGCTCCGTGTA GGNCC-R GGCGACAACTACTTCCTGGT GGNNCC-LCTCACGCCCTGCTCCGTGTA GGNNCC-R GGGCGACAACTACTTCCTGG GGNNNCC-LCCTCTTCAGGGCCGGGGTGG GGNNNCC-R GAGGACCCAGGTGGAACTGC PCSK9 (human) GGCC-LTCAGCTCCAGGCGGTCCTGG GGCC-R AGCAGCAGCAGCAGTGGCAG GGNCC-LTGGGCACCGTCAGCTCCAGG GGNCC-R CAGCAGTGGCAGCGGCCACC GGNNCC-LACCTCTCCCCTGGCCCTCAT GGNNCC-R CCAGGACCGCCTGGAGCTGA GGNNNCC-LCCGTCAGCTCCAGGCGGTCC GGNNNCC-R AGCAGCAGCAGCAGTGGCAG PPP1R3C (PTG) GGCC-LATGTGCCAAGCAAAGCCTCA (human) GGCC-R TTCGGTCATGCCCGTGGATG GGNCC-LGTCGTTGAAATTCATCGTAC GGNCC-R ACCACCTGTGAAGAGTTTCC GGNNCC-LCGTCGTTGAAATTCATCGTA GGNNCC-R ACCACCTGTGAAGAGTTTCC Gys1 (mouse) GGCC-LGAACGCAGTGCTTTTCGAGG GGCC-R ACCCTTGTTGGCCACCTCCC GGNCC-LGGTGACAACTACTATCTGGT GGNCC-R CTCACACCCTGCTCCGTGTA GGNNCC-LGGGTGACAACTACTATCTGG GGNNCC-R CTCACACCCTGCTCCGTGTA GGNNNCC-LCGAGAACGCAGTGCTTTTCG GGNNNCC-R ACCCTTGTTGGCCACCTCCC PPP1R3C (PTG) GGCC-LATGAGCCAAGCAAATCCTCA (mouse) GGCC-R TTCCGTCATGCCCGTGGACA GGNCC-LCTTCGTTGAAAACCATTGTA GGNCC-R CCACCTCTGAAGAGTTTCCT GGNNCC-LCTTCGTTGAAAACCATTGTA GGNNCC-R ACCACCTCTGAAGAGTTTCC GGNNNCC-LCTTCCACTCACTCTGCGATT GGNNNCC-R ACCATGTCTCAGTGTCAAGC PCSK9 (mouse) GGCC-LGGCGGCAACAGCGGCAACAG GGCC-R ACTGCTCTGCGTGGCTGCGG GGNNCC-LCCGCAGCCACGCAGAGCAGT GGNNCC-R GCACCTCTCCTCGCCCCGAT

Alternative Strategies for Improving Stability of Guide RNA andIncreasing Specificity

1. Nucleotides in the 5′ of the guide RNA may be linked via thiolesterlinkages rather than phosphoester linkage like in natural RNA.Thiolester linkage may prevent the guide RNA from being digested byendogenous RNA degradation machinery.

2. Nucleotides in the guide sequence (5′ 20 bp) of the guide RNA can usebridged nucleic acids (BNA) as the bases to improve the bindingspecificity.

Example 30 CRISPR-Cas for Rapid, Multiplex Genome Editing

Aspects of the invention relate to protocols and methods by whichefficiency and specificity of gene modification may be tested within 3-4days after target design, and modified clonal cell lines may be derivedwithin 2-3 weeks.

Programmable nucleases are powerful technologies for mediating genomealteration with high precision. The RNA-guided Cas9 nuclease from themicrobial CRISPR adaptive immune system can be used to facilitateefficient genome editing in eukaryotic cells by simply specifying a20-nt targeting sequence in its guide RNA. Applicants describe a set ofprotocols for applying Cas9 to facilitate efficient genome editing inmammalian cells and generate cell lines for downstream functionalstudies. Beginning with target design, efficient and specific genemodification can be achieved within 3-4 days, and modified clonal celllines can be derived within 2-3 weeks.

The ability to engineer biological systems and organisms holds enormouspotential for applications across basic science, medicine, andbiotechnology. Programmable sequence-specific endonucleases thatfacilitate precise editing of endogenous genomic loci are now enablingsystematic interrogation of genetic elements and causal geneticvariations in a broad range of species, including those that have notbeen genetically tractable previously. A number of genome editingtechnologies have emerged in recent years, including zinc fingernucleases (ZFNs), transcription activator-like effector nucleases(TALENs), and the RNA-guided CRISPR-Cas nuclease system. The first twotechnologies use a common strategy of tethering endonuclease catalyticdomains to modular DNA-binding proteins for inducing targeted DNA doublestranded breaks (DSB) at specific genomic loci. By contrast, Cas9 is anuclease guided by small RNAs through Watson-Crick base-pairing withtarget DNA, presenting a system that is easy to design, efficient, andwell-suited for high-throughput and multiplexed gene editing for avariety of cell types and organisms. Here Applicants describe a set ofprotocols for applying the recently developed Cas9 nuclease tofacilitate efficient genome editing in mammalian cells and generate celllines for downstream functional studies.

Like ZFNs and TALENs, Cas9 promotes genome editing by stimulating DSB atthe target genomic loci. Upon cleavage by Cas9, the target locusundergoes one of two major pathways for DNA damage repair, theerror-prone non-homologous end joining (NHEJ) or the high-fidelityhomology directed repair (HDR) pathway. Both pathways may be utilized toachieve the desired editing outcome.

NHEJ: In the absence of a repair template, the NHEJ process re-ligatesDSBs, which may leave a scar in the form of indel mutations. Thisprocess can be harnessed to achieve gene knockouts, as indels occurringwithin a coding exon may lead to frameshift mutations and a prematurestop codon. Multiple DSBs may also be exploited to mediate largerdeletions in the genome.

HDR: Homology directed repair is an alternate major DNA repair pathwayto NHEJ. Although HDR typically occurs at lower frequencies than NHEJ,it may be harnessed to generate precise, defined modifications at atarget locus in the presence of an exogenously introduced repairtemplate. The repair template may be either in the form of doublestranded DNA, designed similarly to conventional DNA targetingconstructs with homology arms flanking the insertion sequence, orsingle-stranded DNA oligonucleotides (ssODNs). The latter provides aneffective and simple method for making small edits in the genome, suchas the introduction of single nucleotide mutations for probing causalgenetic variations. Unlike NHEJ. HDR is generally active only individing cells and its efficiency varies depending on the cell type andstate.

Overview of CRISPR: The CRISPR-Cas system, by contrast, is at minimum atwo-component system consisting of the Cas9 nuclease and a short guideRNA. Re-targeting of Cas9 to different loci or simultaneous editing ofmultiple genes simply requires cloning a different 20-bpoligonucleotide. Although specificity of the Cas9 nuclease has yet to bethoroughly elucidated, the simple Watson-Crick base-pairing of theCRISPR-Cas system is likely more predictable than that of ZFN or TA LENdomains.

The type II CRISPR-Cas (clustered regularly interspaced shortpalindromic repeats) is a bacterial adaptive immune system that usesCas9, to cleave foreign genetic elements. Cas9 is guided by a pair ofnon-coding RNAs, a variable crRNA and a required auxiliary tracrRNA. ThecrRNA contains a 20-nt guide sequence determines specificity by locatingthe target DNA via Watson-Crick base-pairing. In the native bacterialsystem, multiple crRNAs are co-transcribed to direct Cas9 againstvarious targets. In the CRISPR-Cas system derived from Streptococcuspyogenes, the target DNA must immediately precede a 5′-NGG/NRGprotospacer adjacent motif (PAM), which can vary for other CRISPRsystems.

CRISPR-Cas is reconstituted in mammalian cells through the heterologousexpression of human codon-optimized Cas9 and the requisite RNAcomponents. Furthermore, the crRNA and tracrRNA can be fused to create achimeric, synthetic guide RNA (sgRNA). Cas9 can thus be re-directedtoward any target of interest by altering the 20-nt guide sequencewithin the sgRNA.

Given its ease of implementation and multiplex capability, Cas9 has beenused to generate engineered eukaryotic cells carrying specific mutationsvia both NHEJ and HDR. In addition, direct injection of sgRNA and mRNAencoding Cas9 into embryos has enabled the rapid generation oftransgenic mice with multiple modified alleles; these results holdpromise for editing organisms that are otherwise geneticallyintractable.

A mutant Cas9 carrying a disruption in one of its catalytic domains hasbeen engineered to nick rather than cleave DNA, allowing forsingle-stranded breaks and preferential repair through HDR, potentiallyameliorating unwanted indel mutations from off-target DSBs.Additionally, a Cas9 mutant with both DNA-cleaving catalytic residuesmutated has been adapted to enable transcriptional regulation in E.coli, demonstrating the potential of functionalizing Cas9 for diverseapplications. Certain aspects of the invention relate to theconstruction and application of Cas9 for multiplexed editing of humancells.

Applicants have provided a human codon-optimized, nuclear localizationsequence-flanked Cas9 to facilitate eukaryotic gene editing. Applicantsdescribe considerations for designing the 20-nt guide sequence,protocols for rapid construction and functional validation of sgRNAs,and finally use of the Cas9 nuclease to mediate both NHEJ- and HDR-basedgenome modifications in human embryonic kidney (HEK-293FT) and humanstem cell (HUES9) lines. This protocol can likewise be applied to othercell types and organisms.

Target selection for sgRNA: There are two main considerations in theselection of the 20-nt guide sequence for gene targeting: 1) the targetsequence should precede the 5′-NGG PAM for S. pyogenes Cas9, and 2)guide sequences should be chosen to minimize off-target activity.Applicants provided an online Cas9 targeting design tool that takes aninput sequence of interest and identifies suitable target sites. Toexperimentally assess off-target modifications for each sgRNA,Applicants also provide computationally predicted off-target sites foreach intended target, ranked according to Applicants' quantitativespecificity analysis on the effects of base-pairing mismatch identity,position, and distribution.

The detailed information on computationally predicted off-target sitesis as follows:

Considerations for Off-target Cleavage Activities: Similar to othernucleases, Cas9 can cleave off-target DNA targets in the genome atreduced frequencies. The extent to which a given guide sequence exhibitoff-target activity depends on a combination of factors including enzymeconcentration, thermodynamics of the specific guide sequence employed,and the abundance of similar sequences in the target genome. For routineapplication of Cas9, it is important to consider ways to minimize thedegree of off-target cleavage and also to be able to detect the presenceof off-target cleavage.

Minimizing off-target activity: For application in cell lines,Applicants recommend following two steps to reduce the degree ofoff-target genome modification. First, using our online CRISPR targetselection tool, it is possible to computationally assess the likelihoodof a given guide sequence to have off-target sites. These analyses areperformed through an exhaustive search in the genome for off-targetsequences that are similar sequences as the guide sequence.Comprehensive experimental investigation of the effect of mismatchingbases between the sgRNA and its target DNA revealed that mismatchtolerance is 1) position dependent—the 8-14 bp on the 3′ end of theguide sequence are less tolerant of mismatches than the 5′ bases, 2)quantity dependent—in general more than 3 mismatches are not tolerated,3) guide sequence dependent—some guide sequences are less tolerant ofmismatches than others, and 4) concentration dependent—off-targetcleavage is highly sensitive to the amount of transfected DNA. TheApplicants' target site analysis web tool (available at the websitegenome-engineering.org/tools) integrates these criteria to providepredictions for likely off-target sites in the target genome. Second,Applicants recommend titrating the amount of Cas9 and sgRNA expressionplasmid to minimize off-target activity.

Detection of off-target activities: Using Applicants' CRISPR targetingweb tool, it is possible to generate a list of most likely off-targetsites as well as primers performing SURVEYOR or sequencing analysis ofthose sites. For isogenic clones generated using Cas9, Applicantsstrongly recommend sequencing these candidate off-target sites to checkfor any undesired mutations. It is worth noting that there may be offtarget modifications in sites that are not included in the predictedcandidate list and full genome sequence should be performed tocompletely verify the absence of off-target sites. Furthermore, inmultiplex assays where several DSBs are induced within the same genome,there may be low rates of translocation events and can be evaluatedusing a variety of techniques such as deep sequencing.

The online tool provides the sequences for all oligos and primersnecessary for 1) preparing the sgRNA constructs, 2) assaying targetmodification efficiency, and 3) assessing cleavage at potentialoff-target sites. It is worth noting that because the U6 RNA polymeraseIII promoter used to express the sgRNA prefers a guanine (G) nucleotideas the first base of its transcript, an extra G is appended at the 5′ ofthe sgRNA where the 20-nt guide sequence does not begin with G.

Approaches for sgRNA construction and delivery: Depending on the desiredapplication, sgRNAs may be delivered as either 1) PCR ampliconscontaining an expression cassette or 2) sgRNA-expressing plasmids.PCR-based sgRNA delivery appends the custom sgRNA sequence onto thereverse PCR primer used to amplify a U6 promoter template. The resultingamplicon may be co-transfected with a plasmid containing Cas9 (PX165).This method is optimal for rapid screening of multiple candidate sgRNAs,as cell transfections for functional testing can be performed mere hoursafter obtaining the sgRNA-encoding primers. Because this simple methodobviates the need for plasmid-based cloning and sequence verification,it is well suited for testing or co-transfecting a large number ofsgRNAs for generating large knockout libraries or other scale-sensitiveapplications. Note that the sgRNA-encoding primers are over 100-bp,compared to the ˜20-bp oligos required for plasmid-based sgRNA delivery.

Construction of an expression plasmid for sgRNA is also simple andrapid, involving a single cloning step with a pair of partiallycomplementary oligonucleotides. After annealing the oligo pairs, theresulting guide sequences may be inserted into a plasmid bearing bothCas9 and an invariant scaffold bearing the remainder of the sgRNAsequence (PX330). The transfection plasmids may also be modified toenable virus production for in vivo delivery.

In addition to PCR and plasmid-based delivery methods, both Cas9 andsgRNA can be introduced into cells as RNA.

Design of repair template: Traditionally, targeted DNA modificationshave required use of plasmid-based donor repair templates that containhomology arms flanking the site of alteration. The homology arms on eachside can vary in length, but are typically longer than 500 bp. Thismethod can be used to generate large modifications, including insertionof reporter genes such as fluorescent proteins or antibiotic resistancemarkers. The design and construction of targeting plasmids has beendescribed elsewhere.

More recently, single-stranded DNA oligonucleotides (ssODNs) have beenused in place of targeting plasmids for short modifications within adefined locus without cloning. To achieve high HDR efficiencies, ssODNscontain flanking sequences of at least 40 bp on each side that arehomologous to the target region, and can be oriented in either the senseor antisense direction relative to the target locus.

Functional Testing

SURVEYOR nuclease assay: Applicants detected indel mutations either bythe SURVEYOR nuclease assay (or PCR amplicon sequencing. Applicantsonline CRISPR target design tool provides recommended primers for bothapproaches. However, SURVEYOR or sequencing primers may also be designedmanually to amplify the region of interest from genomic DNA and to avoidnon-specific amplicons using NCBI Primer-BLAST. SURVEYOR primers shouldbe designed to amplify 300-400 bp (for a 600-800 bp total amplicon) oneither side of the Cas9 target for allowing clear visualization ofcleavage bands by gel electrophoresis. To prevent excessive primer dimerformation, SURVEYOR primers should be designed to be typically under25-nt long with melting temperatures of −60° C. Applicants recommendtesting each pair of candidate primers for specific PCR amplicons aswell as for the absence of non-specific cleavage during the SURVEYORnuclease digestion process.

Plasmid- or ssODN-mediated HDR: HDR can be detected viaPCR-amplification and sequencing of the modified region. PCR primers forthis purpose should anneal outside the region spanned by the homologyarms to avoid false detection of residual repair template (HDR Fwd andRev, FIG. 30). For ssODN-mediated HDR, SURVEYOR PCR primers can be used.

Detection of indels or HDR by sequencing: Applicants detected targetedgenome modifications by either Sanger or next-generation deep sequencing(NGS). For the former, genomic DNA from modified region can be amplifiedusing either SURVEYOR or HDR primers. Amplicons should be subcloned intoa plasmid such as pUC19 for transformation; individual colonies can besequenced to reveal clonal genotype.

Applicants designed next-generation sequencing (NGS) primers for shorteramplicons, typically in the 100-200 bp size range. For detecting NHEJmutations, it is important to design primers with at least 10-20 bpbetween the priming regions and the Cas9 target site to allow detectionof longer indels. Applicants provide guidelines for a two-step PCRmethod to attach barcoded adapters for multiplex deep sequencing.Applicants recommend the Illumina platform, due to its generally lowlevels of false positive indels. Off-target analysis (describedpreviously) can then be performed through read alignment programs suchas ClustalW, Geneious, or simple sequence analysis scripts.

Materials and Reagents

sgRNA Preparation:

UltraPure DNaseRNase-free distilled water (Life Technologies, cat. no.10977-023)

Herculase II fusion polymerase (Agilent Technologies, cat. no. 600679)

CRITICAL. Standard Taq polymerase, which lacks 3′-5′ exonucleaseproofreading activity, has lower fidelity and can lead to amplificationerrors. Herculase II is a high-fidelity polymerase (equivalent fidelityto Pfu) that produces high yields of PCR product with minimaloptimization. Other high-fidelity polymerases may be substituted.

Herculase II reaction buffer (5×; Agilent Technologies, included withpolymerase)

dNTP solution mix (25 mM each; Enzymatics, cat. no. N205L)

MgCl2 (25 mM; ThermoScientific, cat. no. R0971)

QIAquick gel extraction kit (Qiagen, cat. no. 28704)

QIAprep spin miniprep kit (Qiagen, cat. no. 27106)

UltraPure TBE buffer (10×; Life Technologies, cat. no. 15581-028)

SeaKem LE agarose (Lonza, cat. no. 50004)

SYBR Safe DNA stain (10,000×; Life Technologies, cat. no. S33102)

1-kb Plus DNA ladder (Life Technologies, cat. no. 10787-018)

TrackIt CyanOrange loading buffer (Life Technologies, cat. no.10482-028)

FastDigest BbsI (BpiI) (Fermentas/ThermoScientific, cat. no. FD1014)

Fermentas Tango Buffer (Fermentas/ThermoScientific, cat. no. BY5)

DL-dithiothreitol (DTT; Fermentas/ThermoScientific, cat. no. R0862)

T7 DNA ligase (Enzymatics, cat. no. L602L)

Critical: Do not substitute the more commonly used T4 ligase. T7 ligasehas 1,000-fold higher activity on the sticky ends than on the blunt endsand higher overall activity than commercially available concentrated T4ligases.

T7 2X Rapid Ligation Buffer (included with T7 DNA ligase, Enzymatics,cat. no. L602L)

T4 Polynucleotide Kinase (New England Biolabs, cat. no M0201S)

T4 DNA Ligase Reaction Buffer (10×; New England Biolabs, cat. no B0202S)

Adenosine 5′-triphosphate (10 mM; New England Biolabs, cat. no. P0756S)

PlasmidSafe ATP-dependent DNase (Epicentre, cat. no. E3101K)

One Shot Stb13 chemically competent Escherichia coli (E. coli) (LifeTechnologies, cat. no. C7373-03)

SOC medium (New England Biolabs, cat. no. B9020S)

LB medium (Sigma, cat. no. L3022)

LB agar medium (Sigma, cat. no. L2897)

Ampicillin, sterile filtered (100 mg ml-l; Sigma, cat. no. A5354)

Mammalian Cell Culture:

HEK293FT cells (Life Technologies, cat. no. R700-07)

Dulbecco's minimum Eagle's medium (DMEM, 1×, high glucose; LifeTechnologies, cat. no. 10313-039)

Dulbecco's minimum Eagle's medium (DMEM, 1×, high glucose, no phenolred; Life Technologies, cat. no. 31053-028)

Dulbecco's phosphate-buffered saline (DPBS, 1×; Life Technologies, cat.no. 14190-250)

Fetal bovine serum, qualified and heat inactivated (Life Technologies,cat. no. 10438-034)

Opti-MEM I reduced-serum medium (FBS; Life Technologies, cat. no.11058-021)

Penicillin-streptomycin (100×; Life Technologies, cat. no. 15140-163)

TrypLE™ Express (1×, no Phenol Red; Life Technologies, cat. no.12604-013)

Lipofectamine 2000 transfection reagent (Life Technologies, cat. no.11668027)

Amaxa SF Cell Line 4D-Nucleofector® X Kit S (32 RCT; Lonza, cat. noV4XC-2032)

HUES 9 cell line (HARVARD STEM CELL SCIENCE)

Geltrex LDEV-Free Reduced Growth Factor Basement Membrane Matrix (LifeTechnologies, cat. no. A1413201)

mTeSR1 medium (Stemcell Technologies, cat. no. 05850)

Accutase cell detachment solution (Stemcell Technologies, cat. no.07920)

ROCK Inhibitor (Y-27632; Millipore, cat. no. SCM075)

Amaxa P3 Primary Cell 4D-Nucleofector® X Kit S (32 RCT; Lonza cat. no.V4XP-3032)

Genotyping Analysis:

QuickExtract DNA extraction solution (Epicentre, cat. no. QE09050)

PCR primers for SURVEYOR, RFLP analysis, or sequencing (see Primertable)

Herculase II fusion polymerase (Agilent Technologies, cat. no. 600679)

CRITICAL. As Surveyor assay is sensitive to single-base mismatches, itis particularly important to use a high-fidelity polymerase. Otherhigh-fidelity polymerases may be substituted.

Herculase II reaction buffer (5×; Agilent Technologies, included withpolymerase)

dNTP solution mix (25 mM each; Enzymatics, cat. no. N205L)

QIAquick gel extraction kit (Qiagen, cat. no. 28704)

Taq Buffer (10×; Genscript, cat. no. B0005)

SURVEYOR mutation detection kit for standard gel electrophoresis(Transgenomic, cat. no. 706025)

UltraPure TBE buffer (10×; Life Technologies, cat. no. 15581-028)

SeaKem LE agarose (Lonza, cat. no. 50004)

4-20% TBE Gels 1.0 mm, 15 Well (Life Technologies, cat. no. EC62255BOX)

Novex® Hi-Density TBE Sample Buffer (5×; Life Technologies, cat. no.LC6678)

SYBR Gold Nucleic Acid Gel Stain (10,000×; Life Technologies, cat. no.S-11494)

1-kb Plus DNA ladder (Life Technologies, cat. no. 10787-018)

TrackIt CyanOrange loading buffer (Life Technologies, cat. no.10482-028)

FastDigest HindIII (Fermentas/ThermoScientific, cat. no. FD0504)

Equipment

Filtered sterile pipette tips (Corning)

Standard 1.5 ml microcentrifuge tubes (Eppendorf, cat. no. 0030 125.150)

Axygen 96-well PCR plates (VWR, cat. no. PCR-96M2-HSC)

Axygen 8-Strip PCR tubes (Fischer Scientific, cat. no. 14-222-250)

Falcon tubes, polypropylene, 15 ml (BD Falcon, cat. no. 352097)

Falcon tubes, polypropylene, 50 ml (BD Falcon, cat. no. 352070)

Round-bottom Tube with cell strainer cap. 5 ml (BD Falcon, cat. no.352235)

Petri dishes (60 mm×15 mm; BD Biosciences, cat. no. 351007)

Tissue culture plate (24 well; BD Falcon, cat. no. 353047)

Tissue culture plate (96 well, flat bottom: BD Falcon, cat. no. 353075)

Tissue culture dish (100 mm; 131BD) Falcon, 353003)

96-well thermocycler with programmable temperature steppingfunctionality (Applied Biosystems Veriti, cat. no. 4375786).

Desktop microcentrifuges 5424, 5804 (Eppendorf)

Gel electrophoresis system (PowerPac basic power supply, Bio-Rad, cat.no. 164-5050, and Sub-Cell GT System gel tray, Bio-Rad, cat. no.170-4401)

Novex XCell SureLock Mini-Cell (Life Technologies, cat. no. EI0001)

Digital gel imaging system (GelDoc EZ, Bio-Rad, cat. no. 170-8270, andblue sample tray, Bio-Rad, cat. no. 170-8273)

Blue light transilluminator and orange filter goggles (SafeImager 2.0;Invitrogen, cat. no. G6600)

Gel quantification software (Bio-Rad, ImageLab, included with GelDoc EZ,or open-source ImageJ from the National Institutes of Health, availableat the website rsbweb.nih.gov/ij/) UV spectrophotometer (NanoDrop 2000c,Thermo Scientific)

Reagent Setup

Tris-borate EDTA (TBE) electrophoresis solution Dilute TBE buffer indistilled water to 1× working solution for casting agarose gels and foruse as a buffer for gel electrophoresis. Buffer may be stored at roomtemperature (18-22° C.) for at least 1 year.

-   -   ATP, 10 mM Divide 10 mM ATP into 50-μl aliquots and store at        −20° C. for up to 1 year; avoid repeated freeze-thaw cycles.    -   DTT, 10 mM Prepare 10 mM DTT solution in distilled water and        store in 20-μl aliquots at −70° C. for up to 2 years; for each        reaction, use a new aliquot, as DTT is easily oxidized.    -   D10 culture medium For culture of HEK293FT cells, prepare D10        culture medium by supplementing DMEM with 1× GlutaMAX and 10%        (vol/vol) fetal bovine serum. As indicated in the protocol, this        medium can also be supplemented with 1× penicillin-streptomycin.        D10 medium can be made in advance and stored at 4° C. for up to        1 month.    -   mTeSR1 culture medium For culture of human embryonic stem cells,        prepare mTeSR1 medium by supplementing the 5× supplement        (included with mTeSR1 basal medium), and 100 ug/ml Normocin.

Procedure

Design of Targeting Components and Use of the Online Tool • Timing 1 d

1| Input target genomic DNA sequence. Applicants provide an online Cas9targeting design tool that takes an input sequence of interest,identifies and ranks suitable target sites, and computationally predictsoff-target sites for each intended target. Alternatively, one canmanually select guide sequence by identifying the 20-bp sequencedirectly upstream of any 5′-NGG.

2| Order necessary oligos and primers as specified by the online tool.If the site is chosen manually, the oligos and primers should bedesigned.

Preparation of sgRNA Expression Construct

3| To generate the sgRNA expression construct, either the PCR- orplasmid-based protocol can be used.

(A) via PCR amplification • Timing 2 h

(i) Applicants prepare diluted U6 PCR template. Applicants recommendusing PX330 as a PCR template, but any U6-containing plasmid maylikewise be used as the PCR template. Applicants diluted template withddH₂O to a concentration of 10 ng/ul. Note that if a plasmid or cassettealready containing an U6-driven sgRNA is used as a template, a gelextraction needs to be performed to ensure that the product containsonly the intended sgRNA and no trace sgRNA carryover from template.

(ii) Applicants prepared diluted PCR oligos. U6-Fwd and U6-sgRNA-Revprimers are diluted to a final concentration of 10 uM in ddH₂O (add 10ul of 100 uM primer to 90 ul ddH₂O).

(iii) U6-sgRNA PCR reaction. Applicants set up the following reactionfor each U6-sgRNA-Rev primer and mastermix as needed:

Component: Amount (ul) Final concentration Herculase II PCR buffer, 5X10 1X dNTP, 100 mM (25 mM each) 0.5 1 mM U6 template (PX330) 1 0.2 ng/ulU6-Fwd primer 1 0.2 uM U6-sgRNA-Rev primer (variable) 1 0.2 uM HerculaseII Fusion polymerase 0.5 Distilled water 36 Total 50

(iv) Applicants performed PCR reaction on the reactions from step (iii)using the following cycling conditions:

Cycle number Denature Anneal Extend  1 95° C., 2 m 2-31 95° C., 20 s 60°C., 20 s 72° C., 20 s 32 72° C., 3 m

(v) After the reaction is completed, Applicants ran the product on a gelto verify successful, single-band amplification. Cast a 2% (wt/vol)agarose gel in 1×TBE buffer with 1× SYBR Safe dye. Run 5 ul of the PCRproduct in the gel at 15 V cm⁻¹ for 20-30 min. Successful ampliconsshould yield one single 370-bp product and the template should beinvisible. It should not be necessary to gel extract the PCR amplicon.

(vi) Applicants purified the PCR product using the QIAquick PCRpurification kit according to the manufacturer's directions. Elute theDNA in 35 ul of Buffer EB or water. Purified PCR products may be storedat 4° C. or −20° C.

(B) Cloning sgRNA into Cas9-Containing Bicistronic Expression Vector •Timing 3 d

(i) Prepare the sgRNA oligo inserts. Applicants resuspended the top andbottom strands of oligos for each sgRNA design to a final concentrationof 100 uM. Phosphorylate and anneal the oligo as follows:

Oligo 1 (100 uM) 1 ul Oligo 2 (100 uM) 1 ul T4 Ligation Buffer, 10X 1 ulT4 PNK 1 ul ddH₂O 6 ul Total 10 ul

(ii) Anneal in a thermocycler using the following parameters:

37° C. for 30 m

95° C. for 5 m

Ramp down to 25° C. at 5° C. per m

(iii) Applicants diluted phosphorylated and annealed oligos 1:200 by add1 ul of oligo to 199 ul room temperature ddH₂O.

(iv) Clone sgRNA oligo into PX330. Applicants set up Golden Gatereaction for each sgRNA. Applicants recommend also setting up ano-insert, PX330 only negative control.

PX330 (100 ng) x ul Diluted oligo duplex from step (iii) 2 ul TangoBuffer, 10X 2 ul DTT, 10 mM 1 ul ATP, 10 mM 1 ul FastDigest BbsI 1 ul T7Ligase 0.5 ul ddH₂O x ul Total 20 ul

(v) Incubate the Golden Gate reaction for a total of 1 h:

Cycle number Condition 1-6 37° C. for 5 m, 21° C. for 5 m

(vi) Applicants treated Golden Gate reaction with PlasmidSafeexonuclease to digest any residual linearized DNA. This step is optionalbut highly recommended.

Golden Gate reaction from step 4 11 ul 10X PlasmidSafe Buffer 1.5 ulATP, 10 mM 1.5 ul PlasmidSafe exonuclease 1 ul Total 15 ul

(vii) Applicants incubated the PlasmidSafe reaction at 37° C. for 30min, followed by inactivation at 70° C. for 30 min. Pause point: aftercompletion, the reaction may be frozen and continued later. The circularDNA should be stable for at least 1 week.

(viii) Transformation. Applicants transformed the PlasmidSafe-treatedplasmid into a competent E. coli strain, according to the protocolsupplied with the cells. Applicants recommend Stb13 for quicktransformation. Briefly, Applicants added 5 ul of the product from step(vii) into 20 ul of ice-cold chemically competent Stb13 cells. This isthen incubated on ice for 10 m, heat shocked at 42° C. for 30 s,returned immediately to ice for 2 m, 100 ul of SOC medium is added, andthis is plated onto an LB plate containing 100 ug/ml ampicillin withincubation overnight at 37° C.

(ix) Day 2: Applicants inspected plates for colony growth. Typically,there are no colonies on the negative control plates (ligation ofBbsI-digested PX330 only, no annealed sgRNA oligo), and tens to hundredsof colonies on the PX330-sgRNA cloning plates.

(x) From each plate, Applicants picked 2-3 colonies to check correctinsertion of sgRNA. Applicants used a sterile pipette tip to inoculate asingle colony into a 3 ml culture of LB medium with 100 ug/mlampicillin. Incubate and shake at 37° C. overnight.

(xi) Day 3: Applicants isolated plasmid DNA from overnight culturesusing a QiAprep Spin miniprep kit according to the manufacturer'sinstructions.

(xii) Sequence validate CRISPR plasmid. Applicants verified the sequenceof each colony by sequencing from the U6 promoter using the U6-Fwdprimer. Optional: sequence the Cas9 gene using primers listed in thefollowing Primer table.

Primer Sequence (5′ to 3′) Purpose U6-For GAGGGCCTATTTCCCATGATTCCAmplify U6- sgRNA. U6-Rev AAAAAAAGCACCGACTCGGTGCCA Amplify U6-CTTTTTCAAGTTGATAACGGACTA sgRNA; N is GCCTTATTTTAACTTGCTATTTCT reverseAGCTCTAAAACNNNNNNNNNNNNN complement NNNNNNCCGGTGTTTCGTCCTTTC of targetCACAAG sgRNA- CACCGNNNNNNNNNNNNNNNNNNN Clone sgRNA top into PX330 sgRNA-AAACNNNNNNNNNNNNNNNNNNNC Clone sgRNA bottom into PX330 U6-AAAAAAAGCACCGACTCGGTGCCA Amplify U6- EMX1- CTTTTTCAAGTTGATAACGGACTAEMX1 sgRNA Rev GCCTTATTTTAACTTGCTATTTCT AGCTCTAAAACCCCTAGTCATTGGAGGTGACCGGTGTTTCGTCCTTTC CACAAG EMX1-top CACCGTCACCTCCAATGACTAGGGClone EMX1 sgRNA into PX330 EMX1- AAACCCCTAGTCATTGGAGGTGAC Clone EMX1bottom sgRNA into PX330 ssODN- CAGAAGAAGAAGGGCTCCCATCAC EMX1 HDR senseATCAACCGGTGGCGCATTGCCACG (sense; AAGCAGGCCAATGGGGAGGACATC insertionGATGTCACCTCCAATGACAAGCTT underlined) GCTAGCGGTGGGCAACCACAAACCCACGAGGGCAGAGTGCTGCTTGCT GCTGGCCAGGCCCCTGCGTGGGCCCAAGCTGGACTCTGGCCACTCCCT ssODN- AGGGAGTGGCCAGAGTCCAGCTTG EMX1 HDRantisense GGCCCACGCAGGGGCCTGGCCAGC (antisense; AGCAAGCAGCACTCTGCCCTCGTGinsertion GGTTTGTGGTTGCCCACCGCTAGC underlined) AAGCTTGTCATTGGAGGTGACATCGATGTCCTCCCCATTGGCCTGCTT CGTGGCAATGCGCCACCGGTTGATGTGATGGGAGCCCTTCTTCTTCTG EMX1- CCATCCCCTTCTGTGAATGT EMX1 SURV-F SURVEYORassay PCR, sequencing EMX1- GGAGATTGGAGACACGGAGA EMX1 SURV-R SURVEYORassay PCR, sequencing EMX1- GGCTCCCTGGGTTCAAAGTA EMX1 RFLP HDR-Fanalysis PCR, sequencing EMX1- AGAGGGGTCTGGATGTCGTAA EMX1 RFLP HDR-Ranalysis PCR, sequencing PUC19-F CGCCAGGGTTTTCCCAGTCACGAC pUC19 multiplecloning site F primer, for Sanger sequencing

Applicants referenced the sequencing results against the PX330 cloningvector sequence to check that the 20 bp guide sequence was insertedbetween the U6 promoter and the remainder of the sgRNA scaffold. Detailsand sequence of the PX330 map in GenBank vector map format (*.gb file)can be found at the website crispr.genome-engineering.org.

(Optional) Design of ssODN Template • Timing 3 d Planning Ahead

3| Design and order ssODN. Either the sense or antisense ssODN can bepurchased directly from supplier. Applicants recommend designinghomology arms of at least 40 bp on either side and 90 bp for optimal HDRefficiency. In Applicants' experience, antisense oligos have slightlyhigher modification efficiencies.

4| Applicants resuspended and diluted ssODN ultramers to a finalconcentration of 10 uM. Do not combine or anneal the sense and antisensessODNs. Store at −20° C.

5| Note for HDR applications, Applicants recommend cloning sgRNA intothe PX330 plasmid.

Functional Validation of sgRNAs: Cell Culture and Transfections • Timing3-4 d

The CRISPR-Cas system has been used in a number of mammalian cell lines.Conditions may vary for each cell line. The protocols below detailstransfection conditions for HEK239FT cells. Note for ssODN-mediated HDRtransfections, the Amaxa SF Cell Line Nucleofector Kit is used foroptimal delivery of ssODNs. This is described in the next section.

7| HEK293FT maintenance. Cells are maintained according to themanufacturer's recommendations. Briefly, Applicants cultured cells inD10 medium (GlutaMax DMEM supplemented with 10% Fetal Bovine Serum), at37° C. and 5% CO2.

8| To passage, Applicants removed medium and rinsed once by gentlyadding DPBS to side of vessel, so as not to dislodge cells. Applicantsadded 2 ml of TrypLE to a T75 flask and incubated for 5 m at 37° C. 10ml of warm D10 medium is added to inactivate and transferred to a 50 mlFalcon tube. Applicants dissociated cells by triturating gently, andre-seeded new flasks as necessary. Applicants typically passage cellsevery 2-3 d at a split ratio of 1:4 or 1:8, never allowing cells toreach more than 70% confluency. Cell lines are restarted upon reachingpassage number 15.

9| Prepare cells for transfection. Applicants plated well-dissociatedcells onto 24-well plates in D10 medium without antibiotics 16-24 hbefore transfection at a seeding density of 1.3×10⁵ cells per well and aseeding volume of 500 ul. Scale up or down according to themanufacturer's manual as needed. It is suggested to not plate more cellsthan recommended density as doing so may reduce transfection efficiency.

10| On the day of transfection, cells are optimal at 70-90% confluency.Cells may be transfected with Lipofectamine 2000 or Amaxa SF Cell LineNucleofector Kit according to the manufacturers' protocols.

(A) For sgRNAs cloned into PX330, Applicants transfected 500 ng ofsequence-verified CRISPR plasmid; if transfecting more than one plasmid,mix at equimolar ratio and no more than 500 ng total.

(B) For sgRNA amplified by PCR, Applicants mixed the following:

PX165 (Cas9 only) 200 ng sgRNA amplicon (each)  40 ng pUC19 fill uptotal DNA to 500 ng

Applicants recommend transfecting in technical triplicates for reliablequantification and including transfection controls (e.g. GFP plasmid) tomonitor transfection efficiency. In addition, PX330 cloning plasmidand/or sgRNA amplicon may be transfected alone as a negative control fordownstream functional assays.

11| Applicants added Lipofectamine complex to cells gently as HEK293FTcells may detach easily from plate easily and result in lowertransfection efficiency.

12| Applicants checked cells 24 h after transfection for efficiency byestimating the fraction of fluorescent cells in the control (e.g., GFP)transfection using a fluorescence microscope. Typically cells are morethan 70% transfected.

13| Applicants supplemented the culture medium with an additional 500 ulof warm D10 medium. Add D10 very slowly to the side of the well and donot use cold medium, as cells can detach easily.

14| Cells are incubated for a total of 48-72 h post-transfection beforeharvested for indel analysis. Indel efficiency does not increasenoticeably after 48 h.

(Optional) Co-Transfection of CRISPR Plasmids and ssODNs or TargetingPlasmids for HR • Timing 3-4 d

15| Linearize targeting plasmid. Targeting vector is linearized ifpossible by cutting once at a restriction site in the vector backbonenear one of the homology arms or at the distal end of either homologyarm.

16| Applicants ran a small amount of the linearized plasmid alongsideuncut plasmid on a 0.8-1% agarose gel to check successful linearization.Linearized plasmid should run above the supercoiled plasmid.

17| Applicants purified linearized plasmid with the QIAQuick PCRPurification kit.

18| Prepare cells for transfection. Applicants cultured HEK293FT in T75or T225 flasks. Sufficient cell count before day of transfection isplanned for. For the Amaxa strip-cuvette format, 2×10⁶ cells are usedper transfection.

19| Prepare plates for transfection. Applicants added 1 ml of warm D10medium into each well of a 12 well plate. Plates are placed into theincubator to keep medium warm.

20| Nucleofection. Applicants transfected HEK293FT cells according tothe Amaxa SF Cell Line Nucleofector 4D Kit manufacturer's instructions,adapted in the steps below.

a. For ssODN and CRISPR cotransfection, pre-mix the following DNA in PCRtubes:

pCRISPR plasmid (Cas9 + sgRNA) 500 ng ssODN template (10 uM) 1 ul

b. For HDR targeting plasmid and CRISPR cotransfection, pre-mix thefollowing DNA in PCR tubes:

CRISPR plasmid (Cas9 + sgRNA) 500 ng Linearized targeting plasmid 500 ng

For transfection controls, see previous section. In addition, Applicantsrecommend transfecting ssODN or targeting plasmid alone as a negativecontrol.

21| Dissociate to single cells. Applicants removed medium and rinsedonce gently with DPBS, taking care not to dislodge cells. 2 ml of TrypLEis added to a T75 flask and incubated for 5 m at 37° C. 10 ml of warmD10 medium is added to inactivate and triturated gently in a 50 mlFalcon tube. It is recommended that cells are triturated gently anddissociated to single cells. Large clumps will reduce transfectionefficiency. Applicants took a 10 ul aliquot from the suspension anddiluted into 90 ul of D10 medium for counting. Applicants counted cellsand calculated the number of cells and volume of suspension needed fortransfection. Applicants typically transfected 2×10⁵ cells per conditionusing the Amaxa Nucleocuvette strips, and recommend calculating for 20%more cells than required to adjust for volume loss in subsequentpipetting steps. The volume needed is transferred into a new Falcontube.

23| Applicants spun down the new tube at 200×g for 5 m.

Applicants prepared the transfection solution by mixing the SF solutionand S supplement as recommended by Amaxa. For Amaxa strip-cuvettes, atotal of 20 ul of supplemented SF solution is needed per transfection.Likewise, Applicants recommend calculating for 20% more volume thanrequired.

25| Applicants removed medium completely from pelleted cells from step23 and gently resuspended in appropriate volume (20 ul per 2×10⁵ cells)of S1-supplemented SF solution. Do not leave cells in SF solution forextended period of time.

26| 20 ul of resuspended cells is pipetted into each DNA pre-mix fromstep 20. Pipette gently to mix and transfer to Nucleocuvette stripchamber. This is repeated for each transfection condition.

Electroporate cells using the Nucleofector 4D program recommended byAmaxa, CM-130.

28| Applicants gently and slowly pipetted 100 ul of warm D10 medium intoeach Nucleocuvette strip chamber, and transferred all volume into thepre-warmed plate from step 19. CRITICAL. Cells are very fragile at thisstage and harsh pipetting can cause cell death. Incubate for 24 h. Atthis point, transfection efficiency can be estimated from fraction offluorescent cells in positive transfection control. Nucleofectiontypically results in greater than 70-80% transfection efficiency.Applicants slowly added 1 ml warm D10 medium to each well withoutdislodging the cells. Incubate cells for a total of 72 h.

Human Embryonic Stem Cell (HUES 9) Culture and Transfection • Timing 3-4d

Maintaining hESC (HUES9) line. Applicants routinely maintain HUES9 cellline in feeder-free conditions with mTesR1 medium. Applicants preparedmTeSR1 medium by adding the 5× supplement included with basal medium and100 ug/ml Normocin. Applicants prepared a 10 ml aliquot of mTeSR1 mediumsupplemented further with 10 uM Rock Inhibitor. Coat tissue cultureplate. Dilute cold GelTrex 1:100 in cold DMEM and coat the entiresurface of a 100 mm tissue culture plate.

Place plate in incubator for at least 30 m at 37° C. Thaw out a vial ofcells at 37° C. in a 15 ml Falcon tube, add 5 ml of mTeSR1 medium, andpellet at 200×g for 5 m. Aspirate off GelTrex coating and seed ˜1×106cells with 10 ml mTeSR1 medium containing Rock Inhibitor. Change tonormal mTeSR1 medium 24 h after transfection and re-feed daily.Passaging cells. Re-feed cells with fresh mTeSR1 medium daily andpassage before reaching 70% confluency. Aspirate off mTeSR1 medium andwash cells once with DPBS. Dissociate cells by adding 2 ml Accutase andincubating at 37° C. for 3-5 m. Add 10 ml mTeSR1 medium to detachedcells, transfer to 15 ml Falcon tube and resuspend gently. Re-plate ontoGelTrex-coated plates in mTeSR1 medium with 10 uM Rock Inhibitor. Changeto normal mTeSR1 medium 24 h after plating.

Transfection. Applicants recommend culturing cells for at least 1 weekpost-thaw before transfecting using the Amaxa P3 Primary Cell 4-DNucleofector Kit (Lonza). Re-feed log-phase growing cells with freshmedium 2 h before transfection. Dissociate to single cells or smallclusters of no more than 10 cells with accutase and gentle resuspension.Count the number of cells needed for nucleofection and spin down at200×g for 5 m. Remove medium completely and resuspend in recommendedvolume of S1-supplemented P3 nucleofection solution. Gently plateelectroporated cells into coated plates in presence of 1× RockInhibitor.

Check transfection success and re-feed daily with regular mTeSR1 mediumbeginning 24 h after nucleofection. Typically, Applicants observegreater than 70% transfection efficiency with Amaxa Nucleofection.Harvest DNA. 48-72 h post transfection, dissociate cells using accutaseand inactivate by adding 5× volume of mTeSR1. Spin cells down at 200×gfor 5 m. Pelleted cells can be directed processed for DNA extractionwith QuickExtract solution. It is recommended to not mechanicallydissociate cells without accutase. It is recommended to not spin cellsdown without inactivating accutase or above the recommended speed; doingso may cause cells to lyse.

Isolation of Clonal Cell Lines by FACS. Timing • 2-3 h Hands-on; 2-3Weeks Expansion

Clonal isolation may be performed 24 h post-transfection by FACS or byserial dilution.

54| Prepare FACS buffer. Cells that do not need sorting using coloredfluorescence may be sorted in regular D10 medium supplemented with 1×penicillin/streptinomycin. If colored fluorescence sorting is alsorequired, a phenol-free DMEM or DPBS is substituted for normal DMEM.Supplement with 1× penicillin/streptinomycin and filter through a 0.22um Steriflip filter.

51| Prepare 96 well plates. Applicants added 100 ul of D10 mediasupplemented with 1× penicillin/streptinomycin per well and prepared thenumber of plates as needed for the desired number of clones.

56| Prepare cells for FACS. Applicants dissociated cells by aspiratingthe medium completely and adding 100 ul TrypLE per well of a 24-wellplate. Incubate for 5 m and add 400 ul warm D10 media.

57| Resuspended cells are transferred into a 15 ml Falcon tube andgently triturated 20 times. Recommended to check under the microscope toensure dissociation to single cells.

58| Spin down cells at 200×g for 5 minutes.

59| Applicants aspirated the media, and resuspended the cells in 200 ulof FACS media.

60| Cells are filtered through a 35 um mesh filter into labeled FACStubes. Applicants recommend using the BD Falcon 12×75 mm Tube with CellStrainer cap. Place cells on ice until sorting.

61| Applicants sorted single cells into 96-well plates prepared fromstep 55. Applicants recommend that in one single designated well on eachplate, sort 100 cells as a positive control.

NOTE. The remainder of the cells may be kept and used for genotyping atthe population level to gauge overall modification efficiency.

62| Applicants returned cells into the incubator and allowed them toexpand for 2-3 weeks. 100 ul of warm D10 medium is added 5 d postsorting. Change 100 ul of medium every 3-5 d as necessary.

63| Colonies are inspected for “clonal” appearance 1 week post sorting:rounded colonies radiating from a central point. Mark off wells that areempty or may have been seeded with doublets or multiplets.

64| When cells are more than 60% confluent, Applicants prepared a set ofreplica plates for passaging. 100 ul of D10 medium is added to each wellin the replica plates. Applicants dissociated cells directly bypipetting up and down vigorously 20 times. 20% of the resuspended volumewas plated into the prepared replica plates to keep the clonal lines.Change the medium every 2-3 d thereafter and passage accordingly.

65| Use the remainder 80% of cells for DNA isolation and genotyping.

Optional: Isolation of Clonal Cell Lines by Dilution. Timing • 2-3 hHands-on; 2-3 Weeks Expansion

66| Applicants dissociated cells from 24-well plates as described above.Make sure to dissociate to single cells. A cell strainer can be used toprevent clumping of cells.

67| The number of cells are counted in each condition. Serially diluteeach condition in D10 medium to a final concentration of 0.5 cells per100 ul. For each 96 well plate, Applicants recommend diluting to a finalcount of 60 cells in 12 ml of D10. Accurate count of cell number isrecommended for appropriate clonal dilution. Cells may be recounted atan intermediate serial dilution stage to ensure accuracy.

68| Multichannel pipette was used to pipette 100 ul of diluted cells toeach well of a 96 well plate.

NOTE. The remainder of the cells may be kept and used for genotyping atthe population level to gauge overall modification efficiency.

69| Applicants inspected colonies for “clonal” appearance ˜1 week postplating: rounded colonies radiating from a central point. Mark off wellsthat may have seeded with doublets or multiplets.

70| Applicants returned cells to the incubator and allowed them toexpand for 2-3 weeks. Re-feed cells as needed as detailed in previoussection.

SURVEYOR Assay for CRISPR Cleavage Efficiency. Timing • 5-6 h

Before assaying cleavage efficiency of transfected cells, Applicantsrecommend testing each new SURVEYOR primer on negative (untransfected)control samples through the step of SURVEYOR nuclease digestion usingthe protocol described below. Occasionally, even single-band cleanSURVEYOR PCR products can yield non-specific SURVEYOR nuclease cleavagebands and potentially interfere with accurate indel analysis.

71| Harvest cells for DNA. Dissociate cells and spin down at 200×g for 5m. NOTE. Replica plate at this stage as needed to keep transfected celllines.

72| Aspirate the supernatant completely.

73| Applicants used QuickExtract DNA extraction solution according tothe manufacturer's instructions. Applicants typically used 50 ul of thesolution for each well of a 24 well plate and 10 ul for a 96 well plate.

74| Applicants normalized extracted DNA to a final concentration of100-200 ng/ul with ddH₂O. Pause point: Extracted DNA may be stored at−20° C. for several months.

75| Set up the SURVEYOR PCR. Master mix the following using SURVEYORprimers provided by Applicants online/computer algorithm tool:

Component: Amount (ul) Final concentration Herculase II PCR buffer, 5X10 1X dNTP, 100 mM (25 mM each) 1 1 mM SURVEYOR Fwd primer (10 uM) 1 0.2uM SURVEYOR Rev primer (10 uM) 1 0.2 uM Herculase II Fusion polymerase 1MgCl₂ (25 mM) 2 1 mM Distilled water 33 Total 49 (for each reaction)

76| Applicants added 100-200 ng of normalized genomic DNA template fromstep 74 for each reaction.

77| PCR reaction was performed using the following cycling conditions,for no more than 30 amplification cycles:

Cycle number Denature Anneal Extend  1 95° C., 2 min 2-31 95° C., 20 s60° C., 20 s 72° C., 30 s 32 72° C., 3 min

78| Applicants ran 2-5 ul of PCR product on a 1% gel to check forsingle-band product. Although these PCR conditions are designed to workwith most pairs of SURVEYOR primers, some primers may need additionaloptimization by adjusting the template concentration, MgCl₂concentration, and/or the annealing temperature.

79| Applicants purified the PCR reactions using the QIAQuick PCRpurification kit and normalized eluant to 20 ng/ul. Pause point:Purified PCR product may be stored at −20° C.

80| DNA heteroduplex formation. The annealing reaction was set up asfollows:

Taq PCR buffer, 10X 2 ul Normalized DNA (20 ng/ul) 18 ul Total volume 20ul

81| Anneal the reaction using the following conditions:

Cycle number Condition 1 95° C., 10 mn 2 95° C.-85° C., −2° C./s 3 85°C., 1 min 4 85° C.-75° C., −0.3° C./s 5 75° C., 1 min 6 75° C.-65° C.,−0.3° C./s 7 65° C., 1 min 8 65° C.-55° C., −0.3° C./s 9 55° C., 1 min10 55° C.-45° C., −0.3° C./s 11 45° C., 1 min 12 45° C.-35° C., −0.3°C./s 13 35° C., 1 min 14 35° C.-25° C., −0.3° C./s 15 25° C., 1 min

82| SURVEYOR nuclease S digestion. Applicants prepared master-mix andadded the following components on ice to annealed heteroduplexes fromstep 81 for a total final volume of 25 ul:

Component Amount (ul) Final Concentration MgCl₂ solution, 0.15 M 2.5 15mM ddH₂O 0.5 SURVEYOR nuclease S 1 1X SURVEYOR enhancer S 1 1X Total 5

83| Vortex well and spin down. Incubate the reaction at 42° C. for 1 h.

84| Optional: 2 ul of the Stop Solution from the SURVEYOR kit may beadded. Pause point. The digested product may be stored at −20° C. foranalysis at a later time.

85| Visualize the SURVEYOR reaction. SURVEYOR nuclease digestionproducts may be visualized on a 2% agarose gel. For better resolution,products may be run on a 4-20% gradient Polyacrylamide TBE gel.Applicants loaded 10 ul of product with the recommended loading bufferand ran the gel according to manufacturer's instructions. Typically,Applicants run until the bromophenol blue dye has migrated to the bottomof the gel. Include DNA ladder and negative controls on the same gel.

86| Applicants stained the gel with 1×SYBR Gold dye diluted in TBE. Thegel was gently rocked for 15 m.

87| Applicants imaged the gel using a quantitative imaging systemwithout overexposing the bands. The negative controls should have onlyone band corresponding to the size of the PCR product, but may haveoccasionally non-specific cleavage bands of other sizes. These will notinterfere with analysis if they are different in size from targetcleavage bands. The sum of target cleavage band sizes, provided byApplicants online/computer algorithm tool, should be equal to the sizeof the PCR product.

88| Estimate the cleavage intensity. Applicants quantified theintegrated intensity of each band using ImageJ or other gelquantification software.

89| For each lane, Applicants calculated the fraction of the PCR productcleaved (f_(cut)) using the following formula: f_(cut)=(b+c)/(a+b+c),where a is the integrated intensity of the undigested PCR product and band c are the integrated intensities of each cleavage product. 901Cleavage efficiency may be estimated using the following formula, basedon the binomial probability distribution of duplex formation:

91|indel (%)=100×(1−√{square root over ((1−f _(cut)))})

Sanger Sequencing for Assessing CRISPR Cleavage Efficiency. Timing. 3 d

Initial steps are identical to Steps 71-79 of the SURVEYOR assay. Note:SURVEYOR primers may be used for Sanger sequencing if appropriaterestriction sites are appended to the Forward and Reverse primers. Forcloning into the recommended pUC19 backbone, EcoRI may be used for theFwd primer and HindIII for the Rev primer.

92| Amplicon digestion. Set up the digestion reaction as follows:

Component Amount (ul) Fast Digest buffer, 10X 3 FastDigest EcoRI 1FastDigest HindIII 1 Normalized DNA (20 ng/ul) 10 ddH₂O 15 Total volume30

93| pUC19 backbone digestion. Set up the digestion reaction as follows:

Component Amount (ul) Fast Digest buffer, 10X 3 FastDigest EcoRI 1FastDigest HindIII 1 FastAP Alkaline Phosphatase 1 pUC19 vector (200ng/ul) 5 ddH₂O 20 Total volume 30

94| Applicants purified the digestion reactions using the QIAQuick PCRpurification kit. Pause point: Purified PCR product may be stored at−20° C.

95| Applicants ligated the digested pUC19 backbone and Sanger ampliconsat a 1:3 vector:insert ratio as follows:

Component Amount (ul) Digested pUC19 x (50 ng) Digested insert x (1:3vector:insert molar ratio) T7 ligase 1 2X Rapid Ligation Buffer 10 ddH₂Ox Total volume 20

96| Transformation. Applicants transformed the PlasmidSafe-treatedplasmid into a competent E. coli strain, according to the protocolsupplied with the cells. Applicants recommend Stb13 for quicktransformation. Briefly, 5 ul of the product from step 95 is added into20 ul of ice-cold chemically competent Stb13 cells, incubated on ice for10 m, heat shocked at 42° C. for 30 s, returned immediately to ice for 2m, 100 ul of SOC medium is added, and plated onto an LB plate containing100 ug/ml ampicillin. This is incubated overnight at 37° C.

97| Day 2: Applicants inspected plates for colony growth. Typically,there are no colonies on the negative control plates (ligation ofEcoRI-HindIII digested pUC19 only, no Sanger amplicon insert), and tensto hundreds of colonies on the pUC19-Sanger amplicon cloning plates.

98| Day 3: Applicants isolated plasmid DNA from overnight cultures usinga QIAprep Spin miniprep kit according to the manufacturer'sinstructions.

99| Sanger sequencing. Applicants verified the sequence of each colonyby sequencing from the pUC19 backbone using the pUC19-For primer.Applicants referenced the sequencing results against the expectedgenomic DNA sequence to check for the presence of Cas9-induced NHEJmutations. % editing efficiency=(# modified clones)/(# total clones). Itis important to pick a reasonable number of clones (>24) to generateaccurate modification efficiencies.

Genotyping for Microdeletion. Timing • 2-3 d Hands on; 2-3 WeeksExpansion

100| Cells were transfected as described above with a pair of sgRNAstargeting the region to be deleted.

101| 24 h post-transfection, clonal lines are isolated by FACS or serialdilution as described above.

102| Cells are expanded for 2-3 weeks.

103| Applicants harvested DNA from clonal lines as described above using10 ul QuickExtract solution and normalized genomic DNA with ddH₂O to afinal concentration of 50-100 ng/ul.

104| PCR Amplify the modified region. The PCR reaction is set up asfollows:

Final Component: Amount (ul) concentration Herculase II PCR buffer, 5X10 1X dNTP, 100 mM (25 mM each) 1  1 mM Out Fwd primer (10 uM) 1 0.2 uMOut Rev primer (10 uM) 1 0.2 uM Herculase II Fusion polymerase 1 MgCl2(25 mM) 2  1 mM ddH₂O 32 Total 48 (for each reaction)

Note: if deletion size is more than 1 kb, set up a parallel set of PCRreactions with In-Fwd and In-Rev primers to screen for the presence ofthe wt allele.

105| To screen for inversions, a PCR reaction is set up as follows:

Final Component: Amount (ul) concentration Herculase II PCR buffer, 5X10 1X dNTP, 100 mM (25 mM each) 1  1 mM Out Fwd or Out-Rev primer (10uM) 1 0.2 uM In Fwd or In-Rev primer (10 uM) 1 0.2 uM Herculase IIFusion polymerase 1 MgCl₂ (25 mM) 2  1 mM ddH₂O 32 Total 48 (for eachreaction)

Note: primers are paired either as Out-Fwd+In Fwd, or Out-Rev+In-Rev.

106| Applicants added 100-200 ng of normalized genomic DNA template fromstep 103 for each reaction.

107| PCR reaction was performed using the following cycling conditions:

Cycle number Denature Anneal Extend 1 95° C., 2 min 2-31 95° C., 20 s60° C., 20 s 72° C., 30 s 32 72° C., 3 m

108| Applicants run 2-5 ul of PCR product on a 1-2% gel to check forproduct. Although these PCR conditions are designed to work with mostprimers, some primers may need additional optimization by adjusting thetemplate concentration, MgCl₂ concentration, and/or the annealingtemperature.

Genotyping for Targeted Modifications Via HDR. Timing ∩ 2-3 d, 2-3 hHands on

109| Applicants harvested DNA as described above using QuickExtractsolution and normalized genomic DNA with TE to a final concentration of100-200 ng/ul.

110| PCR Amplify the modified region. The PCR reaction is set up asfollows:

Component: Amount (ul) Final concentration Herculase II PCR buffer, 5X10 1X dNTP, 100 mM (25 mM each) 1  1 mM HDR Fwd primer (10 uM) 1 0.2 uMHDR Rev primer (10 uM) 1 0.2 uM Herculase II Fusion polymerase 1 MgCl₂(25 mM) 2  1 mM ddH₂O 33 Total 49 (for each reaction)

111| Applicants added 100-200 ng of genomic DNA template from step 109for each reaction and run the following program.

Cycle number Denature Anneal Extend 1 95° C., 2 min 2-31 95° C., 20 s60° C., 20 s 72° C., 30-60 s per kb 32 72° C., 3 min

112| Applicants ran 5 ul of PCR product on a 0.8-1% gel to check forsingle-band product. Primers may need additional optimization byadjusting the template concentration, MgCl₂ concentration, and/or theannealing temperature.

113| Applicants purified the PCR reactions using the QIAQuick PCRpurification kit.

114| In the HDR example, a HindIII restriction site is inserted into theEMX1 gene. These are detected by a restriction digest of the PCRamplicon:

Component Amount (ul) Purified PCR amplicon (200-300 ng) x F.D. buffer,Green 1 HindIII 0.5 ddH2O x Total 10

i. The DNA is digested for 10 m at 37° C.:

ii. Applicants ran 10 ul of the digested product with loading dye on a4-20% gradient polyacrylamide TBE gel until the xylene cyanol band hadmigrated to the bottom of the gel.

iii. Applicants stained the gel with 1×SYBR Gold dye while rocking for15 m.

iv. The cleavage products are imaged and quantified as described abovein the SURVEYOR assay section. HDR efficiency is estimated by theformula: (b+c)/(a+b+c), where a is the integrated intensity for theundigested HDR PCR product, and b and c are the integrated intensitiesfor the HindIII-cut fragments.

115| Alternatively, purified PCR amplicons from step 113 may be clonedand genotyped using Sanger sequencing or NGS.

Deep Sequencing and Off-Target Analysis • Timing 1-2 d

The online CRISPR target design tool generates candidate genomicoff-target sites for each identified target site. Off-target analysis atthese sites can be performed by SURVEYOR nuclease assay, Sangersequencing, or next-generation deep sequencing. Given the likelihood oflow or undetectable modification rates at many of these sites,Applicants recommend deep sequencing with the Illumina Miseq platformfor high sensitivity and accuracy. Protocols will vary with sequencingplatform; here, Applicants briefly describe a fusion PCR method forattaching sequencing adapters.

116| Design deep sequencing primers. Next-generation sequencing (NGS)primers are designed for shorter amplicons, typically in the 100-200 bpsize range. Primers may be manually designed using NCBI Primer-Blast orgenerated with online CRISPR target design tools (website atgenome-engineering.org/tools).

117| Harvest genomic DNA from Cas9-targeted cells. NormalizeQuickExtract genomic DNA to 100-200 ng/ul with ddH2O.

118| Initial library preparation PCR. Using the NGS primers from step116, prepare the initial library preparation PCR

Component: Amount (ul) Final concentration Herculase II PCR buffer, 5X10 1X dNTP, 100 mM (25 mM each) 1  1 mM NGS Fwd primer (10 uM) 1 0.2 uM NGS Rev primer (10 uM) 1 0.2 uM  Herculase II Fusion polymerase 1 MgCl2(25 mM) 2  1 mM ddH2O 33 Total 49 (for each reaction)

119| Add 100-200 ng of normalized genomic DNA template for eachreaction.

120|Perform PCR reaction using the following cycling conditions, for nomore than 20 amplification cycles:

Cycle number Denature Anneal Extend 1 95° C., 2 min 2-21 95° C., 20 s60° C., 20 s 72° C., 15 s 27 72° C., 3 min

121| Run 2-5 ul of PCR product on a 1% gel to check for single-bandproduct. As with all genomic DNA PCRs, NGS primers may requireadditional optimization by adjusting the template concentration, MgCl₂concentration, and/or the annealing temperature.

122| Purify the PCR reactions using the QIAQuick PCR purification kitand normalize eluant to 20 ng/ul. Pause point: Purified PCR product maybe stored at −20° C.

123| Nextera AT DNA Sample Preparation Kit. Following the manufacturer'sprotocol, generate Miseq sequencing-ready libraries with unique barcodesfor each sample.

124| Analyze sequencing data. Off-target analysis may be performedthrough read alignment programs such as ClustalW, Geneious, or simplesequence analysis scripts.

Timing

Steps 1-2 Design and synthesis of sgRNA oligos and ssODNs: 1-5 d,variable depending on supplier

Steps 3-5 Construction of CRISPR plasmid or PCR expression cassette: 2 hto 3 d

Steps 6-53 Transfection into cell lines: 3 d (1 h hands-on time)

Steps 54-70 Optional derivation of clonal lines: 1-3 weeks, variabledepending on cell type

Steps 71-91 Functional validation of NHEJ via SURVEYOR: 5-6 h

Steps 92-124 Genotyping via Sanger or next-gen deep sequencing: 2-3 d(3-4 h hands on time)

Addressing Situations Concerning Herein Examples

Situation Solution No amplification of Titrate U6-template concentrationsgRNA SURVEYOR or HDR Titrate MgCl2; normalize and titrate PCR dirty ortemplate concentration; annealing no amplification temp gradient;redesign primers Unequal amplification Set up separate PCRs to detectwildtype of alleles in and deletion alleles; Redesign primersmicrodeletion PCRs with similar sized amplicons Colonies on IncreaseBbsI; increase Golden Gate reaction negative cycle number, cut PX330separately with control plate Antarctic Phosphate treatment No sgRNAsequences Screen additional colonies or wrong sequences Lowlipofectamine Check cell health and density; titrate DNA; transfectionefficiency add GFP transfection control Low nucleofection Check cellhealth and density; titrate DNA; transfection efficiency suspend tosingle cell Clumps or no cells Filter cells before FACS; dissociate tosingle after FACS cells; resuspend in appropriate density Clumps or nocells Recount cells; dissociate to single cells and in serial dilutionfilter through strainer; check serial dilution High SURVEYOR. Redesignprimers to prime from different background on locations negative sampleDirty SURVEYOR Purify PCR product; reduce input DNA; result on gelreduce 42° C. incubation to 30 m No Purify and normalize PCR product;SURVEYOR re-anneal with TaqB buffer; cleavage Redesign sgRNAs; sequenceverify Cas9 on px330 backbone Samples do not Supplement with MgCl2 to afinal sink in TBE concentration of 15 mM or add acrylamide gel loadingbuffer containing glycerol

Discussion

CRISPR-Cas may be easily multiplexed to facilitate simultaneousmodification of several genes and mediate chromosomal microdeletions athigh efficiencies. Applicants used two sgRNAs to demonstratesimultaneous targeting of the human GRIN2B and DYRK1A loci atefficiencies of up to 68% in HEK293FT cells. Likewise, a pair of sgRNAsmay be used to mediate microdeletions, such as excision of an exon,which can be genotyped by PCR on a clonal level. Note that the preciselocation of exon junctions can vary. Applicants also demonstrated theuse of ssODNs and targeting vector to mediate HDR with both wildtype andnickase mutant of Cas9 in HEK 293FT and HUES9 cells (FIG. 30). Note thatApplicants have not been able to detect HDR in HUES9 cells using theCas9 nickase, which may be due to low efficiency or a potentialdifference in repair activities in HUES9 cells. Although these valuesare typical, there is some variability in the cleavage efficiency of agiven sgRNA, and on rare occasions certain sgRNAs may not work forreasons yet unknown. Applicants recommend designing two sgRNAs for eachlocus, and testing their efficiencies in the intended cell type.

Example 31 NLSs

Cas9 Transcriptional Modulator: Applicants set out to turn the Cas9/gRNACRISPR system into a generalized DNA binding system in which functionsbeyond DNA cleavage can be executed. For instance, by fusing functionaldomain(s) onto a catalytically inactive Cas9 Applicants have impartednovel functions, such as transcriptional activation/repression,methylation/demethylation, or chromatin modifications. To accomplishthis goal Applicants made a catalytically inactive Cas9 mutant bychanging two residues essential for nuclease activity, D10 and H840, toalanine. By mutating these two residues the nuclease activity of Cas9 isabolished while maintaining the ability to bind target DNA. Thefunctional domains Applicants decided to focus on to test Applicants'hypothesis are the transcriptional activator VP64 and thetranscriptional repressors SID and KRAB.

Cas9 Nuclear localization: Applicants hypothesized that the mosteffective Cas9 transcriptional modulator would be strongly localized tothe nucleus where it would have its greatest influence on transcription.Moreover, any residual Cas9 in the cytoplasm could have unwantedeffects. Applicants determined that wild-type Cas9 does not localizeinto the nucleus without including multiple nuclear localization signals(NLSs) (although a CRISPR system need not have one or more NLSs butadvantageously has at least one or more NLS(s)). Because multiple NLSsequences were required it was reasoned that it is difficult to get Cas9into the nucleus and any additional domain that is fused to Cas9 coulddisrupt the nuclear localization. Therefore, Applicants made fourCas9-VP64-GFP fusion constructs with different NLS sequences(pXRP02—pLenti2-EF1a-NLS-hSpCsn1 (10A,840A)-NLS-VP64-EGFP,pXRP04—pLenti2-EF1a-NLS-hSpCsn1(10A,840A)-NLS-VP64-2A-EGFP-NLS,pXRP06—pLenti2-EF1a-NLS-EGFP-VP64-NLS-hSpCsn1(10A,840A)-NLS,pXRP08—pLenti2-EF1a-NLS-VP64-NLS-hSpCsn1(10A,840A)-NLS-VP64-EGFP-NLS).These constructs were cloned into a lenti backbone under the expressionof the human EF1a promoter. The WPRE element was also added for morerobust protein expression. Each construct was transfected into HEK 293FTcells using Lipofectame 2000 and imaged 24 hours post-transfection. Thebest nuclear localization is obtained when the fusion proteins have NLSsequences on both the N- and C-term of the fusion protein. The highestobserved nuclear localization occurred in the construct with four NLSelements.

To more robustly understand the influence of NLS elements on Cas9Applicants made 16 Cas9-GFP fusions by adding the same alpha importin NLS sequence on either the N- or C-term looking at zero to three tandemrepeats. Each construct was transfected into HEK 293FT cells usingLipofectame 2000 and imaged 24 hours post-transfection. Notably, thenumber of NLS elements does not directly correlate with the extent ofnuclear localization. Adding an NLS on the C-term has a greaterinfluence on nuclear localization than adding on the N-term.

Cas9 Transcriptional Activator: Applicants functionally tested theCas9-VP64 protein by targeting the Sox2 locus and quantifyingtranscriptional activation by RT-qPCR. Eight DNA target sites werechosen to span the promoter of Sox2. Each construct was transfected intoHEK 293FT cells using Lipofectame 2000 and 72 hours post-transfectiontotal RNA was extracted from the cells. 1 ug of RNA was reversetranscribed into cDNA (qScript Supermix) in a 40 ul reaction. 2 ul ofreaction product was added into a single 20 ul TaqMan assay qPCRreaction. Each experiment was performed in biological and technicaltriplicates. No RT control and no template control reactions showed noamplification. Constructs that do not show strong nuclear localization,pXRP02 and pXRP04, result in no activation. For the construct that didshow strong nuclear localization, pXRP08, moderate activation wasobserved. Statistically significant activation was observed in the caseof guide RNAs Sox2.4 and Sox2.5.

Example 32 In Vivo Mouse Data

Material and Reagents

Herculase II fusion polymerase (Agilent Technologies, cat. no. 600679)10× NEBuffer 4 (NEB, cat. No. B7004S)BsaI HF (NEB, cat. No. R3535S)T7 DNA ligase (Enzymatics, cat. no. L602L)Fast Digest buffer, 10× (ThermoScientific, cat. No. B64)FastDigest NotI (ThermoScientific, cat. No. FD0594)FastAP Alkaline Phosphatase (ThermoScientific, cat. No. EF0651)Lipofectamine-2000 (Life Technologies, cat. No. 11668-019)Trypsin (Life Technologies, cat. No. 15400054)Forceps #4 (Sigma, cat. No. Z168777-1EA)Forceps #5 (Sigma, cat. No. F6521-1EA)10× Hank's Balanced Salt Solution (Sigma, cat. No. H4641-500M L)Penicillin/Streptomycin solution (Life Technologies, cat. No. P4333)Neurobasal (Life Technologies, cat. No. 21103049)B27 Supplement (Life Technologies, cat. No. 17504044)L-glutamine (Life Technologies, cat. No. 25030081)Glutamate (Sigma, cat. No. RES5063G-A7)β-mercaptoethanol (Sigma, cat. No. M6250-100mL)HA rabbit antibody (Cell Signaling, cat. No. 3724S)LIVE/DEAD® Cell Imaging Kit (Life Technologies, cat. No. R37601)30G World Precision Instrument syringe (World Precision Instruments,cat. No. NANOFIL)Stereotaxic apparatus (Kopf Instruments)UltraMicroPump3 (World Precision Instruments, cat. No. UMP3-4)Sucrose (Sigma, cat. No. S7903)Calcium chloride (Sigma, cat. No. C1016)Magnesium acetate (Sigma, cat. No. M0631)

Tris-HCl (Sigma, cat. no T5941)

EDTA (Sigma, cat. No. E6758)NP-40 (Sigma, cat. No. NP40)Phenylmethanesulfonyl fluoride (Sigma, cat. No. 78830)Magnesium chloride (Sigma, cat. No. M8266)Potassium chloride (Sigma, cat. No. P9333)β-glycerophosphate (Sigma, cat. No. G9422)Glycerol (Sigma, cat. No. G9012)Vybrant® DyeCycle™ Ruby Stain (Life technologies, cat. No. S4942)FACS Aria Flu-act-cell sorter (Koch Institute of MIT, Cambridge US)DNAeasy Blood & Tissue Kit (Qiagen, cat. No. 69504)

Procedure

Constructing gRNA Multiplexes for Using In Vivo in the Brain

Applicants designed and PCR amplified single gRNAs targeting mouse TETand DNMT family members (as described herein) Targeting efficiency wasassessed in N2a cell line (FIG. 33). To obtain simultaneous modificationof several genes in vivo, efficient gRNA was multiplexed inAAV-packaging vector (FIG. 34). To facilitate further analysis of systemefficiency applicants added to the system expression cassette consistentof GFP-KASH domain fusion protein under control of human Synapsin Ipromoter (FIG. 34). This modification allows for further analysis ofsystem efficiency in neuronal population (more detail procedure insection Sorting nuclei and in vivo results).

All 4 parts of the system were PCR amplified using Herculase II Fusionpolymerase using following primers:

1st U6 7w: gagggtctcgtccttgcggccgcgctagcgagggcctatttcccatgatt c1st gRNA Rv: ctcggtctcggtAAAAAAgcaccgactcggtgccactttttcaagttgataacggactagccttattttaacttgctaTTTCtagctctaaaacNNNNNNNNNNNNNNNNNNNNGGTGTTTCGTCCTTTCCAC 2nd U6 Fw:gagggtctaTTTaccggtgagggcctatttcccatgattcc 2nd gRNA Rv:ctcggtctcctcAAAAAAgcaccgactcggtgccactttttcaagttgataacggactagc cttattttaacttgctaTTTCtagctctaaaacNNNNNNNNNNNNNNNNNNNNGGTGTTTCGTCCTTTCCAC 3rd U6 Fw:gagggtctcTTTgagctcgagggcctatttcccatgattc 3rd gRNA Rv:ctcggtctcgcgtAAAAAAgcaccgactcggtgccactttttcaagttgataacggactag ccttattttaacttgctaTTTCtagctctaaaacNNNNNNNNNNNNNNNNNNNNGGTGTTTCGTCCTTTCCA hSyn_GFP-kash Fw:gagggtctcTTacgcgtgtgtctagac hSyn_GFP-kash Rv:ctcggtctcAaggaCAGGGAAGGGAGCAGTGGTTCACGCCTGTAATCCCAGCAATTTGGGA GGCCAAGGTGGGTAGATCACCTGAGATTAGGAGTTGC(NNNNNNNNNNNNNNNNNNNN is a reverse compliment targeted genomic sequence)

Applicants used Golden Gate strategy to assemble all parts (1:1molecular ratio) of the system in a single step reaction:

l^(st) U6_gRNA  18 ng 2^(nd) U6_gRNA  18 ng 3^(rd) U6_gRNA  18 ngSyn_GFP-kash 100 ng 10x NEBuffer 4 1.0 μl 10x BSA 1.0 μl 10 mM ATP 1.0μl BsaI HF 0.75 μl  T7 ligase 0.25 μl  ddH₂O  10 μl Cycle numberCondition 1-50 37° C. for 5 m, 21° C. for 5 m

Golden Gate reaction product was PCR amplified using Herculase II fusionpolymerase and following primers:

Fw 5′cctgtccttgcggccgcgctagcgagggc Rv 5′cacgcggccgcaaggacagggaagggagcag

PCR product was cloned into AAV backbone, between ITR sequences usingNotI restriction sites:

PCR Product Digestion:

Fast Digest buffer, 10X 3 μl FastDigest NotI 1 μl DNA  1 μg ddH₂O up to30 μl

AAV Backbone Digestion:

Fast Digest buffer, 10X 3 μl FastDigest NotI 1 μl FastAP AlkalinePhosphatase 1 μl AAV backbone  1 μg ddH₂O up to 30 μl

After 20 min incubation in 37° C. samples were purified using QiAQuickPCR purification kit. Standardized samples were ligated at a 1:3vector:insert ratio as follows:

Digested pUC19 50 ng  Digested insert 1:3 vector:insert molar ratio T7ligase 1 μl 2X Rapid Ligation Buffer 5 μl ddH₂0 up to 10 μl

After transformation of bacteria with ligation reaction product,applicants confirmed obtained clones with Sanger sequencing.

Positive DNA clones were tested in N2a cells after co-transfection withCas9 construct (FIGS. 35 and 36).

Design of New Cas9 Constructs for AAV Delivery

AAV delivery system despite its unique features has packinglimitation—to successfully deliver expressing cassette in vivo it has tobe in size < then 4.7 kb. To decrease the size of SpCas9 expressingcassette and facilitate delivery applicants tested several alteration:different promoters, shorter polyA signal and finally a smaller versionof Cas9 from Staphylococcus aureus (SaCas9) (FIGS. 37 and 38). Alltested promoters were previously tested and published to be active inneurons, including mouse Mecp2 (Gray et al., 2011), rat Map1b andtruncated rat Map1b (Liu and Fischer, 1996). Alternative synthetic polyAsequence was previously shown to be functional as well (Levitt et al.,1989; Gray et al., 2011). All cloned constructs were expressed in N2acells after transfection with Lipofectamine 2000, and tested withWestern blotting method (FIG. 39).

Testing AAV Multiplex System in Primary Neurons

To confirm functionality of developed system in neurons, Applicants useprimary neuronal cultures in vitro. Mouse cortical neurons was preparedaccording to the protocol published previously by Banker and Goslin(Banker and Goslin, 1988).

Neuronal cells are obtained from embryonic day 16. Embryos are extractedfrom the euthanized pregnant female and decapitated, and the heads areplaced in ice-cold HBSS. The brains are then extracted from the skullswith forceps (#4 and #5) and transferred to another change of ice-coldHBSS. Further steps are performed with the aid of a stereoscopicmicroscope in a Petri dish filled with ice-cold HBSS and #5 forceps. Thehemispheres are separated from each other and the brainstem and clearedof meninges. The hippocampi are then very carefully dissected and placedin a 15 ml conical tube filled with ice-cold HBSS. Cortices that remainafter hippocampal dissection can be used for further cell isolationusing an analogous protocol after removing the brain steam residuals andolfactory bulbs. Isolated hippocampi are washed three times with 10 mlice-cold HBSS and dissociated by 15 min incubation with trypsin in HBSS(4 ml HBSS with the addition of 10 μl 2.5% trypsin per hippocampus) at37° C. After trypsinization, the hippocampi are very carefully washedthree times to remove any traces of trypsin with HBSS preheated to 37°C. and dissociated in warm HBSS. Applicants usually dissociate cellsobtained from 10-12 embryos in 1 ml HBSS using 1 ml pipette tips anddilute dissociated cells up to 4 ml. Cells are plated at a density of250 cells/mm2 and cultured at 37° C. and 5% CO2 for up to 3 week

HBSS

435 ml H20 50 ml 10× Hank's Balanced Salt Solution 16.5 ml 0.3M HEPES pH7.3

5 ml penicillin-streptomycin solutionFilter (0.2 μm) and store 4° C.

Neuron Plating Medium (100 ml)

97 ml Neurobasal 2 ml B27 Supplement

1 ml penicillin-streptomycin solution250 μl glutamine125 μl glutamateNeurons are transduced with concentrated AAV1/2 virus or AAV1 virus fromfiltered medium of HEK293FT cells, between 4-7 days in culture and keepfor at least one week in culture after transduction to allow fordelivered gene expression.

AAV-Driven Expression of the System

Applicants confirmed expression of SpCas9 and SaCas9 in neuronalcultures after AAV delivery using Western blot method (FIG. 42). Oneweek after transduction neurons were collected in NuPage SDS loadingbuffer with β-mercaptoethanol to denaturate proteins in 95° C. for 5min. Samples were separated on SDS PAGE gel and transferred on PVDFmembrane for WB protein detection. Cas9 proteins were detected with HAantibody.

Expression of Syn-GFP-kash from gRNA multiplex AAV was confirmed withfluorescent microscopy (FIG. 50).

Toxicity

To assess the toxicity of AAV with CRISPR system Applicants testedoverall morphology of neurons one week after virus transduction (FIG.45). Additionally, Applicants tested potential toxicity of designedsystem with the LIVE/DEAD® Cell Imaging Kit, which allows to distinguishlive and dead cells in culture. It is based on the presence ofintracellular esterase activity (as determined by the enzymaticconversion of the non-fluorescent calcein AM to the intensely greenfluorescent calcein). On the other hand, the red, cell-impermeantcomponent of the Kit enters cells with damaged membranes only and bindto DNA generating fluorescence in dead cells. Both fluorophores can beeasily visualized in living cells with fluorescent microscopy.AAV-driven expression of Cas9 proteins and multiplex gRNA constructs inthe primary cortical neurons was well tolerated and not toxic (FIGS. 43and 44), what indicates that designed AAV system is suitable for in vivotests.

Virus Production

Concentrated virus was produced according to the methods described inMcClure et al., 2011. Supernatant virus production occurred in HEK293FTcells.

Brain Surgeries

For viral vector injections 10-15 week old male C57BL/6N mice wereanesthetized with a Ketamine/Xylazine cocktail (Ketamine dose of 100mg/kg and Xylazine dose of 10 mg/kg) by intraperitoneal injection.Intraperitonial administration of Buprenex was used as a pre-emptiveanalgesic (1 mg/kg). Animals were immobilized in a Kopf stereotaxicapparatus using intra-aural positioning studs and tooth bar to maintainan immobile skull. Using a hand-held drill, a hole (1-2 mm) at −3.0 mmposterior to Bregma and 3.5 mm lateral for injection in the CA1 regionof the hippocampus was made. Using 30G World Precision Instrumentsyringe at a depth of 2.5 mm, the solution of AAV viral particles in atotal volume of 1 ul was injected. The injection was monitored by a‘World Precision Instruments UltraMicroPump3’ injection pump at a flowrate of 0.5 ul/min to prevent tissue damage. When the injection wascomplete, the injection needle was removed slowly, at a rate of 0.5mm/min. After injection, the skin was sealed with 6-0 Ethilon sutures.Animals were postoperatively hydrated with 1 mL lactated Ringer's(subcutaneous) and housed in a temperature controlled (37° C.)environment until achieving an ambulatory recovery. 3 weeks aftersurgery animals were euthanized by deep anesthesia followed by tissueremoval for nuclei sorting or with 4% paraformaldehyde perfusion forimmunochemistry.

Sorting Nuclei and In Vivo Results

Applicants designed a method to specifically genetically tag the gRNAtargeted neuronal cell nuclei with GFP for Fluorescent Activated CellSorting (FACS) of the labeled cell nuclei and downstream processing ofDNA, RNA and nuclear proteins. To that purpose the applicants' multiplextargeting vector was designed to express both a fusion protein betweenGFP and the mouse nuclear membrane protein domain KASH (Starr DA, 2011,Current biology) and the 3 gRNAs to target specific gene loci ofinterest (FIG. 34). GFP-KASH was expressed under the control of thehuman Synapsin promoter to specifically label neurons. The amino acid ofthe fusion protein GFP-KASH was:

MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYKSGLRSREEEEETDSRMPHLDSPGSSQPRRSFLSRVIRAALPLQLLLLLLLLLACLLPASEDDYSCTQANNFARSFYPMLRYTNGPPPT

One week after AAV1/2 mediated delivery into the brain a robustexpression of GFP-KASH was observed. For FACS and downstream processingof labeled nuclei, the hippocampi were dissected 3 weeks after surgeryand processed for cell nuclei purification using a gradientcentrifugation step. For that purpose the tissue was homogenized in 320mM Sucrose, 5 mM CaCl, 3 mM Mg(Ac)2, 10 mM Tris pH 7.8, 0.1 mM EDTA,0.1% NP40, 0.1 mM Phenylmethanesulfonyl fluoride (PMSF), 1 mM3-mercaptoethanol using 2 ml Dounce homogenizer (Sigma) The homogenisatewas centrifuged on a 25% to 29% Optiprep® gradient according to themanufacture's protocol for 30 min at 3.500 rpm at 4° C. The nuclearpellet was resuspended in 340 mM Sucrose, 2 mM MgCl2, 25 mM KCl, 65 mMglycerophosphate, 5% glycerol, 0.1 mM PMSF, 1 mM β-mercaptoethanol andVybrant®; DyeCycle™ Ruby Stain (Life technologies) was added to labelcell nuclei (offers near-infrared emission for DNA). The labeled andpurified nuclei were sorted by FACS using an Aria Flu-act-cell sorterand BDFACS Diva software. The sorted GFP+ and GFP− nuclei were finallyused to purify genomic DNA using DNAeasy Blood & Tissue Kit (Qiagen) forSurveyor assay analysis of the targeted genomic regions. The sameapproach can be easily used to purify nuclear RNA or protein fromtargeted cells for downstream processing. Due to the 2-vector system(FIG. 34) the applicants using in this approach efficient Cas9 mediatedDNA cleavage was expected to occur only in a small subset of cells inthe brain (cells which were co-infected with both the multiplextargeting vector and the Cas9 encoding vector). The method describedhere enables the applicants to specifically purify DNA, RNA and nuclearproteins from the cell population expressing the 3 gRNAs of interest andtherefore are supposed to undergo Cas9 mediated DNA cleavage. By usingthis method the applicants were able to visualize efficient DNA cleavagein vivo occurring only in a small subset of cells.

Essentially, what Applicants have shown here is targeted in vivocleavage. Furthermore, Applicants used a multiple approach, with severaldifferent sequences targeted at the same time, but independently.Presented system can be applied for studying brain pathologic conditions(gene knock out, e.g. Parkinson disease) and also open a field forfurther development of genome editing tools in the brain. By replacingnuclease activity with gene transcription regulators or epigeneticregulators it will be possible to answer whole spectrum of scientificquestion about role of gene regulation and epigenetic changes in thebrain in not only in the pathologic conditions but also in physiologicalprocess as learning and memory formation. Finally, presented technologycan be applied in more complex mammalian system as primates, what allowsto overcome current technology limitations.

Example 33 Model Data

Several disease models have been specifically investigated. Theseinclude de novo autism risk genes CHD8, KATNAL2, and SCN2A; and thesyndromic autism (Angelman Syndrome) gene UBE3A. These genes andresulting autism models are of course preferred, but show that theinvention may be applied to any gene and therefore any model ispossible.

Applicants have made these cells lines using Cas9 nuclease in humanembryonic stem cells (hESCs). The lines were created by transienttransfection of hESCs with Cbh-Cas9-2A-EGFP and pU6-sgRNA. Two sgRNAsare designed for each gene targeting most often the same exons in whichpatient nonsense (knock-out) mutations have been recently described fromwhole exome sequencing studies of autistic patients. The Cas9-2A-EGFPand pU6 plasmids were created specifically for this project.

Example 34 AAV Production System or Protocol

An AAV production system or protocol that was developed for, and worksparticularly well with, high through put screening uses is providedherein, but it has broader applicability in the present invention aswell. Manipulating endogenous gene expression presents variouschallenges, as the rate of expression depends on many factors, includingregulatory elements, mRNA processing, and transcript stability. Toovercome this challenge, Applicants developed an adeno-associated virus(AAV)-based vector for the delivery. AAV has an ssDNA-based genome andis therefore less susceptible to recombination.

AAV1/2 (serotype AAV1/2, i.e., hybrid or mosaic AAV1/AAV2 capsid AAV)heparin purified concentrated virus protocol

Media: D10+HEPES

500 ml bottle DMEM high glucose+Glutamax (GIBCO)50 ml Hyclone FBS (heat-inactivated) (Thermo Fischer)5.5 ml HEPES solution (1M, GIBCO)Cells: low passage HEK293FT (passage <10 at time of virus production,thaw new cells of passage 2-4 for virus production, grow up for 3-5passages)

Transfection Reagent: Polyethylenimine (PEI) “Max”

Dissolve 50 mg PEI “Max” in 50 ml sterile Ultrapure H20

Adjust pH to 7.1

Filter with 0.22 um fliptop filterSeal tube and wrap with parafilmFreeze aliquots at −20° C. (for storage, can also be used immediately)

Cell Culture

Culture low passage HEK293FT in D10+HEPESPassage everyday between 1:2 and 1:2.5Advantageously do not allow cells to reach more than 85% confluency

For T75

Warm 10 ml HBSS (—Mg2+, —Ca2+, GIBCO)+1 ml TrypLE Express (GIBCO) perflask to 37° C. (Waterbath)

Aspirate media fully

Add 10 ml warm HBSS gently (to wash out media completely)

Add 1 ml TrypLE per Flask

Place flask in incubator (37° C.) for 1 min

Rock flask to detach cells

Add 9 ml D10+HEPES media (37° C.)

Pipette up and down 5 times to generate single cell suspension

Split at 1:2-1:2.5 (12 ml media for T75) ratio (if cells are growingmore slowly, discard and thaw a new batch, they are not in optimalgrowth)

transfer to T225 as soon as enough cells are present (for ease ofhandling large amounts of cells)

AAV Production (5*15 Cm Dish Scale Per Construct):

Plate 10 million cells in 21.5 ml media into a 15 cm dishIncubate for 18-22 hours at 37° C.Transfection is ideal at 80% confluence

Per Plate

Prewarm 22 ml media (D10+HEPES)

Prepare Tube with DNA Mixture (Use Endofree Maxiprep DNA):

5.2 ug vector of interest plasmid4.35 ug AAV 1 serotype plasmid4.35 ug AAV 2 serotype plasmid10.4 ug pDF6 plasmid (adenovirus helper genes) □ Vortex to mixAdd 434 uL DMEM (no serum!)Add 130 ul PEI solutionVortex 5-10 secondsAdd DNA/DMEM/PEI mixture to prewarmed mediaVortex briefly to mixReplace media in 15 cm dish with DNA/DMEM/PEI mixtureReturn to 37° C. incubatorIncubate 48 h before harvesting (make sure medium isn't turning tooacidic)

Virus Harvest:

1. aspirate media carefully from 15 cm dish dishes (advantageously donot dislodge cells)2. Add 25 ml RT DPBS (Invitrogen) to each plate and gently remove cellswith a cell scraper. Collect suspension in 50 ml tubes.3. Pellet cells at 800×g for 10 minutes.4. Discard supernatant

Pause Point: Freeze Cell Pellet at −80 C if Desired

5. resuspend pellet in 150 mM NaCl, 20 mM Tris pH 8.0, use 10 ml pertissue culture plate.6. Prepare a fresh solution of 10% sodium deoxycholate in dH2O. Add 1.25ml of this per tissue culture plate for a final concentration of 0.5%.Add benzonase nuclease to a final concentration of 50 units per ml. Mixtube thoroughly.7. Incubate at 37° C. for 1 hour (Waterbath).8. Remove cellular debris by centrifuging at 3000×g for 15 mins.Transfer to fresh 50 ml tube and ensure all cell debris has been removedto prevent blocking of heparin columns.

Heparin Column Purification of AAV1/2:

1. Set up HiTrap heparin columns using a peristaltic pump so thatsolutions flow through the column at 1 ml per minute. It is important toensure no air bubbles are introduced into the heparin column.

2. Equilibrate the column with 10 ml 150 mM NaCl, 20 mM Tris, pH 8.0using the peristaltic pump.

3. Binding of virus: Apply 50 ml virus solution to column and allow toflow through.

4. Wash step 1: column with 20 ml 100 mM NaCl, 20 mM Tris, pH 8.0.(using the peristaltic pump)

5. Wash step 2: Using a 3 ml or 5 ml syringe continue to wash the columnwith 1 ml 200 mM NaCl, 20 mM Tris, pH 8.0, followed by 1 ml 300 mM NaCl,20 mM Tris, pH 8.0.

Discard the flow-through.

(prepare the syringes with different buffers during the 50 min flowthrough of virus solution above)

6. Elution Using 5 ml syringes and gentle pressure (flow rate of <1ml/min) elute the virus from the column by applying:

1.5 ml 400 mM NaCl, 20 mM Tris, pH 8.0

3.0 ml 450 mM NaCl, 20 mM Tris, pH 8.0

1.5 ml 500 mM NaCl, 20 mM Tris, pH 8.0

Collect these in a 15 ml centrifuge tube.

Concentration of AAV1/2:

1. Concentration step 1: Concentrate the eluted virus using Amicon ultra15 ml centrifugal filter units with a 100,000 molecular weight cutoff.Load column eluate into the concentrator and centrifuge at 2000×g for 2minutes (at room temperature. Check concentrated volume—it should beapproximately 500 μl. If necessary, centrifuge in 1 min intervals untilcorrect volume is reached.

2. buffer exchange: Add 1 ml sterile DPBS to filter unit, centrifuge in1 min intervals until correct volume (500 ul) is reached.

3. Concentration step 2: Add 500 ul concentrate to an Amicon Ultra 0.5ml 100K filter unit. Centrifuge at 6000 g for 2 min. Check concentratedvolume—it should be approximately 100 μl. If necessary, centrifuge in 1min intervals until correct volume is reached.

4. Recovery: Invert filter insert and insert into fresh collection tube.Centrifuge at 1000 g for 2 min.

Aliquot and freeze at −80 C1 μl is typically required per injection site, small aliquots (e.g. 5ul) are therefore recommended (avoid freeze-thaw of virus).determine DNaseI-resistant GC particle titer using qPCR (see separateprotocol)

Materials

Amicon Ultra, 0.5 ml, 100K; MILLIPORE; UFC510024 Amicon Ultra, 15 ml,100K; MILLIPORE; UFC910024

Benzonase nuclease; Sigma-Aldrich, E1014HiTrap Heparin cartridge; Sigma-Aldrich; 54836Sodium deoxycholate; Sigma-Aldrich; D5670

AAV1 Supernatant Production Protocol

Media: D10+HEPES

500 ml bottle DMEM high glucose+Glutamax (Invitrogen)50 ml Hyclone FBS (heat-inactivated) (Thermo Fischer)5.5 ml HEPES solution (1M, GIBCO)Cells: low passage HEK293FT (passage <10 at time of virus production)Thaw new cells of passage 2-4 for virus production, grow up for 2-5passagesTransfection reagent: Polyethylenimine (PEI) “Max”Dissolve 50 mg PEI “Max” in 50 ml sterile Ultrapure H20

Adjust pH to 7.1

Filter with 0.22 um fliptop filterSeal tube and wrap with parafilmFreeze aliquots at −20° C. (for storage, can also be used immediately)

Cell Culture

Culture low passage HEK293FT in D10+HEPES Passage everyday between 1:2and 1:2.5Advantageously do let cells reach more than 85% confluency

For T75

Warm 10 ml HBSS (—Mg2+, —Ca2+, GIBCO)+1 ml TrypLE Express (GIBCO) perflask to 37° C. (Waterbath)

Aspirate media fully

Add 10 ml warm HBSS gently (to wash out media completely)

Add 1 ml TrypLE per Flask

Place flask in incubator (37° C.) for 1 min

Rock flask to detach cells

Add 9 ml D10+HEPES media (37° C.)

Pipette up and down 5 times to generate single cell suspension

Split at 1:2-1:2.5 (12 ml media for T75) ratio (if cells are growingmore slowly, discard and thaw a new batch, they are not in optimalgrowth)

transfer to T225 as soon as enough cells are present (for ease ofhandling large amounts of cells)

AAV production (single 15 cm dish scale)Plate 10 million cells in 21.5 ml media into a 15 cm dishIncubate for 18-22 hours at 37° C.Transfection is ideal at 80% confluence per platePrewarm 22 ml media (D10+HEPES)Prepare tube with DNA mixture (use endofree maxiprep DNA):5.2 ug vector of interest plasmid8.7 ug AAV1 serotype plasmid10.4 ug DF6 plasmid (adenovirus helper genes)

Vortex to mix

Add 434 uL DMEM (no serum!) Add 130 ul PEI solutionVortex 5-10 secondsAdd DNA/DMEM/PEI mixture to prewarmed mediaVortex briefly to mixReplace media in 15 cm dish with DNA/DMEM/PEI mixtureReturn to 37° C. incubatorIncubate 48 h before harvesting (advantageously monitor to ensure mediumis not turning too acidic)

Virus Harvest:

Remove supernatant from 15 cm dishFilter with 0.45 um filter (low protein binding) Aliquot and freeze at−80° C.Transduction (primary neuron cultures in 24-well format, 5DIV)Replace complete neurobasal media in each well of neurons to betransduced with fresh neurobasal (usually 400 ul out of 500 ul per wellis replaced)Thaw AAV supernatant in 37° C. waterbathLet equilibrate in incubator for 30 minAdd 250 ul AAV supernatant to each well

Incubate 24 h at 37° C.

Remove media/supernatant and replace with fresh complete neurobasalExpression starts to be visible after 48 h, saturates around 6-7 DaysPost InfectionConstructs for pAAV plasmid with GOI should not exceed 4.8 kb includingboth ITRS.

Example of a human codon optimized sequence (i.e. being optimized forexpression in humans) sequence: SaCas9 is provided below:

ACCGGTGCCACCATGTACCCATACGATGTTCCAGATTACGCTTCGCCGAAGAAAAAGCGCAAGGTCGAAGCGTCCATGAAAAGGAACTACATTCTGGGGCTGGACATCGGGATTACAAGCGTGGGGTATGGGATTATTGACTATGAAACAAGGGACGTGATCGACGCAGGCGTCAGACTGTTCAAGGAGGCCAACGTGGAAAACAATGAGGGACGGAGAAGCAAGAGGGGAGCCAGGCGCCTGAAACGACGGAGAAGGCACAGAATCCAGAGGGTGAAGAAACTGCTGTTCGATTACAACCTGCTGACCGACCATTCTGAGCTGAGTGGAATTAATCCTTATGAAGCCAGGGTGAAAGGCCTGAGTCAGAAGCTGTCAGAGGAAGAGTTTTCCGCAGCTCTGCTGCACCTGGCTAAGCGCCGAGGAGTGCATAACGTCAATGAGGTGGAAGAGGACACCGGCAACGAGCTGTCTACAAAGGAACAGATCTCACGCAATAGCAAAGCTCTGGAAGAGAAGTATGTCGCAGAGCTGCAGCTGGAACGGCTGAAGAAAGATGGCGAGGTGAGAGGGTCAATTAATAGGTTCAAGACAAGCGACTACGTCAAAGAAGCCAAGCAGCTGCTGAAAGTGCAGAAGGCTTACCACCAGCTGGATCAGAGCTTCATCGATACTTATATCGACCTGCTGGAGACTCGGAGAACCTACTATGAGGGACCAGGAGAAGGGAGCCCCTTCGGATGGAAAGACATCAAGGAATGGTACGAGATGCTGATGGGACATTGCACCTATTTTCCAGAAGAGCTGAGAAGCGTCAAGTACGCTTATAACGCAGATCTGTACAACGCCCTGAATGACCTGAACAACCTGGTCATCACCAGGGATGAAAACGAGAAACTGGAATACTATGAGAAGTTCCAGATCATCGAAAACGTGTTTAAGCAGAAGAAAAAGCCTACACTGAAACAGATTGCTAAGGAGATCCTGGTCAACGAAGAGGACATCAAGGGCTACCGGGTGACAAGCACTGGAAAACCAGAGTTCACCAATCTGAAAGTGTATCACGATATTAAGGACATCACAGCACGGAAAGAAATCATTGAGAACGCCGAACTGCTGGATCAGATTGCTAAGATCCTGACTATCTACCAGAGCTCCGAGGACATCCAGGAAGAGCTGACTAACCTGAACAGCGAGCTGACCCAGGAAGAGATCGAACAGATTAGTAATCTGAAGGGGTACACCGGAACACACAACCTGTCCCTGAAAGCTATCAATCTGATTCTGGATGAGCTGTGGCATACAAACGACAATCAGATTGCAATCTTTAACCGGCTGAAGCTGGTCCCAAAAAAGGTGGACCTGAGTCAGCAGAAAGAGATCCCAACCACACTGGTGGACGATTTCATTCTGTCACCCGTGGTCAAGCGGAGCTTCATCCAGAGCATCAAAGTGATCAACGCCATCATCAAGAAGTACGGCCTGCCCAATGATATCATTATCGAGCTGGCTAGGGAGAAGAACAGCAAGGACGCACAGAAGATGATCAATGAGATGCAGAAACGAAACCGGCAGACCAATGAACGCATTGAAGAGATTATCCGAACTACCGGGAAAGAGAACGCAAAGTACCTGATTGAAAAAATCAAGCTGCACGATATGCAGGAGGGAAAGTGTCTGTATTCTCTGGAGGCCATCCCCCTGGAGGACCTGCTGAACAATCCATTCAACTACGAGGTCGATCATATTATCCCCAGAAGCGTGTCCTTCGACAATTCCTTTAACAACAAGGTGCTGGTCAAGCAGGAAGAGAACTCTAAAAAGGGCAATAGGACTCCTTTCCAGTACCTGTCTAGTTCAGATTCCAAGATCTCTTACGAAACCTTTAAAAAGCACATTCTGAATCTGGCCAAAGGAAAGGGCCGCATCAGCAAGACCAAAAAGGAGTACCTGCTGGAAGAGCGGGACATCAACAGATTCTCCGTCCAGAAGGATTTTATTAACCGGAATCTGGTGGACACAAGATACGCTACTCGCGGCCTGATGAATCTGCTGCGATCCTATTTCCGGGTGAACAATCTGGATGTGAAAGTCAAGTCCATCAACGGCGGGTTCACATCTTTTCTGAGGCGCAAATGGAAGTTTAAAAAGGAGCGCAACAAAGGGTACAAGCACCATGCCGAAGATGCTCTGATTATCGCAAATGCCGACTTCATCTTTAAGGAGTGGAAAAAGCTGGACAAAGCCAAGAAAGTGATGGAGAACCAGATGTTCGAAGAGAAGCAGGCCGAATCTATGCCCGAAATCGAGACAGAACAGGAGTACAAGGAGATTTTCATCACTCCTCACCAGATCAAGCATATCAAGGATTTCAAGGACTACAAGTACTCTCACCGGGTGGATAAAAAGCCCAACAGAGAGCTGATCAATGACACCCTGTATAGTACAAGAAAAGACGATAAGGGGAATACCCTGATTGTGAACAATCTGAACGGACTGTACGACAAAGATAATGACAAGCTGAAAAAGCTGATCAACAAAAGTCCCGAGAAGCTGCTGATGTACCACCATGATCCTCAGACATATCAGAAACTGAAGCTGATTATGGAGCAGTACGGCGACGAGAAGAACCCACTGTATAAGTACTATGAAGAGACTGGGAACTACCTGACCAAGTATAGCAAAAAGGATAATGGCCCCGTGATCAAGAAGATCAAGTACTATGGGAACAAGCTGAATGCCCATCTGGACATCACAGACGATTACCCTAACAGTCGCAACAAGGTGGTCAAGCTGTCACTGAAGCCATACAGATTCGATGTCTATCTGGACAACGGCGTGTATAAATTTGTGACTGTCAAGAATCTGGATGTCATCAAAAAGGAGAACTACTATGAAGTGAATAGCAAGTGCTACGAAGAGGCTAAAAAGCTGAAAAAGATTAGCAACCAGGCAGAGTTCATCGCCTCCTTTTACAACAACGACCTGATTAAGATCAATGGCGAACTGTATAGGGTCATCGGGGTGAACAATGATCTGCTGAACCGCATTGAAGTGAATATGATTGACATCACTTACCGAGAGTATCTGGAAAACATGAATGATAAGCGCCCCCCTCGAATTATCAAAACAATTGCCTCTAAGACTCAGAGTATCAAAAAGTACTCAACCGACATTCTGGGAAACCTGTATGAGGTGAAGAGCAAAAAGCACCCTCAGATTATCAAAAAGGGCTAAGAAT TC

Example 35 Minimizing Off Target Cleavage Using Cas9 Nickase and TwoGuide RNAs

Cas9 is a RNA-guided DNA nuclease that may be targeted to specificlocations in the genome with the help of a 20 bp RNA guide. However theguide sequence may tolerate some mismatches between the guide sequenceand the DNA-target sequence. The flexibility is undesirable due to thepotential for off-target cleavage, when the guide RNA targets Cas9 to aan off-target sequence that has a few bases different from the guidesequence. For all experimental applications (gene targeting, cropengineering, therapeutic applications, etc) it is important to be ableto improve the specificity of Cas9 mediated gene targeting and reducethe likelihood of off-target modification by Cas9.

Applicants developed a method of using a Cas9 nickase mutant incombination with two guide RNAs to facilitate targeted double strandbreaks in the genome without off-target modifications. The Cas9 nickasemutant may be generated from a Cas9 nuclease by disabling its cleavageactivity so that instead of both strands of the DNA duplex being cleavedonly one strand is cleaved. The Cas9 nickase may be generated byinducing mutations in one or more domains of the Cas9 nuclease, e.g.Ruvc1 or HNH. These mutations may include but are not limited tomutations in a Cas9 catalytic domain, e.g in SpCas9 these mutations maybe at positions D10 or H840. These mutations may include but are notlimited to D10A, E762A, H840A. N854A, N863A or D986A in SpCas9 butnickases may be generated by inducing mutations at correspondingpositions in other CRISPR enzymes or Cas9 orthologs. In a most preferredembodiment of the invention the Cas9 nickase mutant is a SpCas9 nickasewith a D10A mutation.

The way this works is that each guide RNA in combination with Cas9nickase would induce the targeted single strand break of a duplex DNAtarget. Since each guide RNA nicks one strand, the net result is adouble strand break. The reason this method eliminates off-targetmutations is because it is very unlikely to have an off-target site thathas high degrees of similarity for both guide sequences (20 bp+2bp(PAM)=22 bp specificity for each guide, and two guides means anyoff-target site will have to have close to 44 bp of homologoussequence). Although it is still likely that individual guides may haveoff-targets, but those off-targets will only be nicked, which isunlikely to be repaired by the mutagenic NHEJ process. Therefore themultiplexing of DNA double strand nicking provides a powerful way ofintroducing targeted DNA double strand breaks without off-targetmutagenic effects.

Applicants carried out experiments involving the co-transfection ofHEK293FT cells with a plasmid encoding Cas9(D10A) nickase as well as DNAexpression cassettes for one or more guides. Applicants transfectedcells using Lipofectamine 2000, and transfected cells were harvested 48or 72 hours after transfections. Double nicking-induced NHEJ weredetected using the SURVEYOR nuclease assay as described previouslyherein (FIGS. 51, 52 and 53).

Applicants have further identified parameters that relate to efficientcleavage by the Cas9 nickase mutant when combined with two guide RNAsand these parameters include but are not limited to the length of the 5′overhang. Efficient cleavage is reported for 5′ overhang of at least 26base pairs. In a preferred embodiment of the invention, the 5′ overhangis at least 30 base pairs and more preferably at least 34 base pairs.Overhangs of up to 200 base pairs may be acceptable for cleavage, while5′ overhangs less than 100 base pairs are preferred and 5′ overhangsless than 50 base pairs are most preferred (FIGS. 54 and 55).

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What is claimed is:
 1. A genome wide library comprising a plurality ofCRISPR-Cas system guide RNAs comprising guide sequences that are capableof targeting a plurality of target sequences in a plurality of genomicloci in a population of eukaryotic cells.
 2. The library of claim 1,wherein the population of cells is a population of embryonic stem (ES)cells.
 3. The library of claim 1, wherein the target sequence in thegenomic locus is a non-coding sequence.
 4. The library of claim 1,wherein gene function of one or more gene products is altered by saidtargeting.
 5. The library of claim 1, wherein said targeting results ina knockout of gene function.
 6. The library of claim 1, wherein thetargeting is of about 100 or more sequences.
 7. The library of claim 1,wherein the targeting is of about 1000 or more sequences.
 8. The libraryof claim 1, wherein the targeting is of about 20,000 or more sequences.9. The library of claim 1, wherein the targeting is of the entiregenome.
 10. The library of claim 1, wherein the targeting is of a panelof target sequences focused on a relevant or desirable pathway.
 11. Thelibrary of claim 10, wherein the pathway is an immune pathway.
 12. Thelibrary of claim 5, wherein targeting is of about 100 or more sequences.13. The library of claim 5, wherein targeting is of about 1000 or moresequences.
 14. The library of claim 5, wherein targeting is of about20,000 or more sequences.
 15. The library of claim 5, wherein targetingis of the entire genome.
 16. The library of claim 5, wherein thetargeting is of a panel of target sequences focused on a relevant ordesirable pathway.
 17. The library of claim 16, wherein the pathway isan immune pathway.
 18. The library of claim 16, wherein the pathway is acell division pathway.
 19. The library of claim 5, wherein the knockoutof gene function comprises: introducing into each cell in the populationof cells a vector system of one or more vectors comprising anengineered, non-naturally occurring CRISPR-Cas system comprising I. aCas protein, and II. one or more guide RNAs, wherein components I and IImay be same or on different vectors of the system, integratingcomponents I and II into each cell, wherein the guide sequence targets aunique gene in each cell, wherein the Cas protein is operably linked toa regulatory element, wherein when transcribed, the guide RNA comprisingthe guide sequence directs sequence-specific binding of a CRISPR-Cassystem to a target sequence in the genomic loci of the unique gene,inducing cleavage of the genomic loci by the Cas protein, and confirmingdifferent knockout mutations in a plurality of unique genes in each cellof the population of cells thereby generating a gene knockout celllibrary.
 20. The library of claim 19, wherein the one or more vectorsare plasmid vectors.
 21. The library of claim 19, wherein the regulatoryelement is an inducible promoter.
 22. The library of claim 19, whereinthe inducible promoter is a doxycycline inducible promoter.
 23. Thelibrary of claim 19, wherein the confirming of different knockoutmutations is by whole exome sequencing.
 24. The library of claim 19,wherein the knockout mutation is achieved in 100 or more unique genes.25. The library of claim 19, wherein the knockout mutation is achievedin 1000 or more unique genes.
 26. The library of claim 19, wherein theknockout mutation is achieved in 20,000 or more unique genes.
 27. Thelibrary of claim 19, wherein the knockout mutation is achieved in theentire genome,
 28. The library of claim 19, wherein the knockout of genefunction is achieved in a plurality of unique genes which function in aparticular physiological pathway or condition.
 29. The library of claim28, wherein the pathway or condition is an immune pathway or condition.30. The library of claim 28, wherein the pathway or condition is a celldivision pathway or condition.